Most of the stations are named after the villages that were closest to the station. Some other stations have more eclectic etymologies, which can be interesting. Some of these stories have larger connects with the history of Mumbai and India as a whole, but I’m not listing those here, and limiting myself to only the station names. I’ll keep adding them here as and when possible:
Acharya Atre Nagar:
Named after prominent orator, film maker & newspaper editor Pralhad Keshav Atre, who as an educationist was also known as Acharya Atre (Teacher/Prof. Atre). More Info: Pralhad Keshav Atre<
The junction where this Metro station is built connects to the Terminal 2 of the Mumbai Airport, and is laconically named Airport Road. More Info: Airport Rd, Chimatpada, Greater Indra Nagar, Andheri East, Mumbai, Maharashtra 400059 – Google Maps
From the Ambarnath/Ambareshwar shrine in the village, present since the 1100s, which also had mango (amba) trees in its courtyard. More Info in  below.
Named after freedom fighter, social reformer, and father of the Indian Constitution Dr. B. R. Ambedkar. More Info: B. R. Ambedkar
Very difficult to get any decent source information on this. Wikipedia says it is named after a hill called Udayanagari, but I find it hard to digest.  below identifies the hill where the Mahakali and Jogeshwari caves are situated as Andhakagiri, from which came Aandheri. Kalpish Ratna’s book Once Upon A Hill calls it Andhragiri, which is more palatable. More Info: Once Upon A Hill and in  below.
Probably the name of the owner of the hill, one N. Antoba (Antoba, or Antob, is listed as a common Indian surname) was corrupted into Antop by the Portugese. This Antoba was a secretary to the Govt. and owned a lot of properties. More Info in  below.
Azad Nagar: No pure etymology is available online, but usually, areas named Azad mean either one of two things; Azad = freedom in Urdu, or named after Maulana Azad, freedom fighter and India’s first education minister. More Info: Abul Kalam Azad
This village was on the trade route between Surat & other parts of Gujarat & the Konkan and other parts of Maharashtra. It was used as a remount depot where warriors would change their plains-experienced horses with those trained for mountain climbing and vice versa. The word in the local language that means ‘to change’ is ‘Badla’, which stuck to the village, and hence it was named Badlapur (pur is a suffix denoting a place – village/town etc.). More info: Badlapur
Bandra & Bandra Terminus:
In all probability, this is a corruption of the word Bandar, which means Port in many languages – both Indian & Colonial European. The Portugese had built a seafacing fort here, whose remnants can be seen at Land’s End at Bandstand. More Info: Bandra
This Monorail Station is close to & services a privately built housing complex named Bhakti Park, which is otherwise quite remotely located on all four sides. More Info: Google Maps
This Monorail Station is built opposite the Bharat Petroleum refinery and is hence named after it. More Info: Google Maps
Mentioned as Bhayndar in the 1800s, and earlier as Binda circa 100 AD, as a port town. More Info in  below.
Mentioned as Bhiwndi, in the 1800s & early 1900s, present as Bhimdi & Bimbri since the early 1500s. More Info in  below.
After some more research, I found that there is no King Byculla of Portugal. So the etymology comes from the bhaya tree (Amaltas, Cassia Fistula) that used to grow here on a plain (khala), or that this was a threshing ground (khala), that belonged to someone named Bhaya. More Info in  below.
Chakala (JB Nagar):
Chakala is one of the oldest villages that formed the original Andheri suburban area. As Chaquelem, it is listed as one of the early Catholic villages in the area in the 1500s. Prior to that, it was also known as Chachale in the Mahikavati era. The second part of the name, JB Nagar, is named after philanthropist & freedom fighter Jamnalal Bajaj. More info: Holy Family Parish, Jamnalal Bajaj and  below.
In 1838, the British introduced a tax on herdsmen who wanted to have their cattle graze on public grounds, that most cattle owners couldn’t afford. Sir Jamsetjee Jeejeebhoy purchased some land near the Thakurdwar area which he then let the herdsmen use for free for grazing. The area started to be known as Charni (Charna in the local languages means to graze). So when a station was constructed here, it was named Charni Road. More Info: Charni Road railway station
Listed since the first century CE (77 AD!!!) as Perimilla to Symulla/Timulla (2nd – 3rd centuries), Chemula (in the Kanheri Caves inscriptions, 300s – 500s), Sibor (5th century) and Saimur(10th – 12th centuries) which must have gotten corrupted to Chimod in the 1800s and Chembur now. More Info in  below.
Chhatrapati Shivaji Terminus:
Originally Bori Bunder station when the Indian Railways started in the 1850s, and the first station ever to be built, it was renamed Victoria Terminus after Queen Victoria. It was renamed Chhatrapati Shivaji Terminus in 1996 after the great Maratha monarch. More Info: Chhatrapati Shivaji Terminus
Chinch = tamarind. Pokli = valley of trees. There seemed to have been a vale of tamarind trees in this area. Once spelled as Chintz Poglie. More Info in  below.
Chuna = Lime, Bhatti = kiln. There were many lime quarries & kilns in this area, giving rise to this name. More Info: A secular milestone for Mumbai
Of the 3 gates of the Fort (now known as the Fort area) the nearest one to the St. Thomas Church (now St. Thomas Cathedral) used to be where Flora Fountain is now. Obviously, it started getting known as the Church Gate. So when the Colaba station was closed and the new station was built, it was built in the Church Gate area and named ‘Churchgate’. More Info: Churchgate
From what I am able to make out of online archives & Wikipedia, India’s first Cotton Exchange started on a village green (a meadow) in the location where Badhwar Park is now. The exchange was supposedly shifted to near where the Cotton Green station is. It kept the name as the Art Deco building it was housed in was painted in a green colour. I think this is anecdotal enough to actually make sense. More Info: Cotton Green
B̶u̶i̶l̶t̶ t̶o̶ C̶a̶r̶r̶y̶ h̶o̶r̶s̶e̶s̶ f̶r̶o̶m̶ t̶h̶e̶ R̶a̶c̶e̶ C̶o̶u̶r̶s̶e̶ t̶o̶ P̶u̶n̶e̶’̶s̶ s̶t̶u̶d̶ f̶a̶r̶m̶s̶. I stand corrected: Named after C. Currey, who was the Agent of the BB&CI Railway from 1865 to 1875. More Info in  below.
Dadar & Dadar East:
Named after a set of stairs (dadar) that were built on the eastern edge of Mahim island, near to where the station was built. More Info: .
Mentioned as Dahanuka, a village and a river, as early as 100 AD, then as Dahanu since the 1500s. More Info in  below.
From the Sanskrit Dadhicheshwar. This would mean that there would have been a temple in this area, dedicated to the saint Dadhichi, who sacrificed his life so that the gods could fashion weapons out of his bones to defeat the asuras. This word was converted to the Prakrit Dahisar by the locals. More Info in  below.
Named after political leader, the first British MP from Asia, and Congress Founder Dadabhai Naoroji. More Info: D.N. Nagar
Dockyard Road: Closest to the shipmaking hub Mazagon Docks Ltd., hence Dockyard. More Info: Dockyard Road railway station
In all probability, named after the Domb tribe, who used to live here, and finds mention from the 1100s and later. More Info: Dombivli
Named after John Elphinstone, 13th Lord Elphinstone and 1st Baron Elphinstone, Governor of Bombay from 1853 to 1860. More Info: Elphinstone Road railway station
Fertilizer Township: This Monorail Station is built next to the Rashtriya Chemicals & Fertilizers Ltd. plant, opposite which a township came up for housing the plant’s workers & staff, appropriately named Fertilizer Township. More info: Google Maps
One root traces it to Ghat-kopra (कोपरा) which means corner of the Western Ghats of the Sahyadri range. I̶ ̶f̶i̶n̶d̶ i̶t̶ d̶i̶f̶f̶i̶c̶u̶l̶t̶ t̶o̶ d̶i̶g̶e̶s̶t̶,̶ g̶i̶v̶e̶n̶ t̶h̶a̶t̶ t̶h̶e̶ G̶h̶a̶t̶s̶ e̶n̶d̶ o̶n̶ t̶h̶e̶ o̶t̶h̶e̶r̶ s̶i̶d̶e̶ o̶f̶ t̶h̶e̶ c̶r̶e̶e̶k̶,̶ i̶n̶ N̶a̶v̶i̶ M̶u̶m̶b̶a̶i̶. I stand corrected – after Jayesh Jagasia’s comment below, I checked a topographic map of the city, and a branch of the Western Ghats does end near Ghatkopar. Ghat (घाट) also means a hilly road, and there are some hills that have to be crossed to reach this area. Hence, both, the dumber explanation of it being a colloquial bastardization of Ghat-ke-oopar (घाट-के-ऊपर), Above-the-ghat, and that of it being a corner of the Western Ghats, make sense. More Info: Ghatkopar
An urban legend traces it to the family name of freedom fighters and social reformers Keshav & Mrinal Gore (Goregaon = Gore’s Village), but the name predates their fame. Another legend traces it to the fairness (gora means fair) of milk, as there are many major dairy farms here, but that is also not true – the dairy farms are pretty recent in history. The third legend traces it to the fairness of foreigners who stayed here, but no sources for that. Truth is, the village existed as Gorgam as early as the 1500s-1600s. Prior to then, it was known as Gorakhgaon in the Mahikavati era. Probably from the founder’s name (someone named Gorakh) or if a temple to Gorakhnath was there. More info: Goregaon and in  below.
Grant Road: Named after Sir Robert Grant, who was Governor of Bombay from 1834 till his death in 1838. More Info: Grant Road railway station
Guru Tegh Bahadur Nagar (GTB Nagar):
The area around the station has been occupied since the time the city was still split into seven islands by fisherfolk – who were identified as Koli people (Koli = fisherman). The village was known as Koliwada (Village of the Koli people), so the station when originally constructed was also called Koliwada. During the 1960’s, it was renamed Guru Tegh Bahadur Nagar after after Guru Tegh Bahadurji, the 9th Sikh Guru, as the local area is now occupied largely by Sikh people, some of whom shifted here when there were fears of war with Pakistan. S̶o̶m̶e̶o̶n̶e̶ ̶s̶a̶i̶d̶ ̶t̶h̶a̶t̶ ̶t̶h̶e̶ ̶s̶t̶a̶t̶i̶o̶n̶ ̶w̶a̶s̶ ̶o̶r̶i̶g̶i̶n̶a̶l̶l̶y̶ ̶n̶a̶m̶e̶d̶ ̶K̶o̶l̶i̶w̶a̶d̶a̶ ̶a̶f̶t̶e̶r̶ ̶t̶h̶e̶ ̶f̶i̶s̶h̶i̶n̶g̶ ̶v̶i̶l̶l̶a̶g̶e̶ ̶n̶o̶w̶ ̶k̶n̶o̶w̶n̶ ̶a̶s̶ ̶S̶i̶o̶n̶ ̶K̶o̶l̶i̶w̶a̶d̶a̶,̶ ̶a̶n̶d̶ ̶l̶a̶t̶e̶r̶ ̶r̶e̶n̶a̶m̶e̶d̶.̶ ̶I̶’̶v̶e̶ ̶f̶o̶u̶n̶d̶ ̶n̶o̶ ̶s̶o̶u̶r̶c̶e̶s̶ ̶f̶o̶r̶ ̶t̶h̶a̶t̶,̶ ̶w̶i̶l̶l̶ ̶u̶p̶d̶a̶t̶e̶ ̶o̶n̶c̶e̶ ̶I̶ ̶d̶o̶.̶ More Info: Guru Tegh Bahadur Nagar & Koli- The native fisher folk of mumbai
Near the current Mahalaxmi station, a traffic circle came up, which has seven roads feeding into it, all leading to major parts of the island city & suburbs. The traffic island that came up at this place was named after a General in the Army, Sir George Le Grand Jacob, whose adopted daughter donated the fountain at the centre of the circle’s garden. The circle itself has been renamed Sant Gadge Maharaj Chowk, but it is still colloquially known by the seven roads feeding into it, aka Saat Rasta. More Info in  below.
Named after the Goddess Yogeshwari (Goddess of knowledge and enlightenment) whose temple is there in the caves in this area, called the Jogeshwari caves. More Info: Jogeshwari Caves
Mentioned as a port by the name of Kallinena in the 2nd – 3rd centuries, as Kaliyan & Kalian in the Kanheri inscriptions in the 2nd – 6th centuries, and as a market city named Kalliana in the sixth century. More Info in  below.
A couple of online sources trace it to Khand, which means stone/rock, as the station was built to service quarries that supplied stones to the Backbay Reclamation project. A better origin, though, is that there was an East Indian Christian village named Condolim since atleast the mid-1600s in the area. Condolim may also be an European corruption of Kandhavali or Kadhevalli Pallika, as it is listed during the Mahikavati era. Both -vali/-valli and Pallika mean villages, and kandha/kadhe is an old name for mangroves, which still grow with abandon on both banks of the Gorai creek nearby. More info: Kandivali and in  below.
Kanjur village is listed as Kanzure in  below. The second part, marg means road in Marathi. So the station could also have been named Kanjur Road for all that matters. More Info in  below.
Mentioned as a part of a twin village/town set Kelve-Mahim (not the Mahikavati Mahim, but another one) since the mid-1300s. The two villages are also mentioned as Quelmain, Kielwe-Mahi, Maim in the 1500s-1600s. More Info in  below.
Named after Khar Danda, the local fishing village nearby. खार (Khaar) colloiqually defines a salty land, which is what the area was, being close to the Arabian sea. More Info: Khar Road
Mentioned as Khopivli in the 1800s, and prior to that as Campoli/Campolee as a village with a temple built by Nana Phadnavis. More Info in  below.
The road that connects Sion to Crawford Market, currently known as Dr. Ambedkar Road, was once planned to be named King’s Way, and the gardens at one end as King’s Circle. Now known as Maheshwari Udyan, this is actually a large traffic circle which has been converted into a public garden. More info: Maheshwari Udyan, Mumbai and in  below. Edited after reading Zainab Kakal’s comment below.
Named Konpre or Kopar, as it is today, in the 12th – 16th centuries CE. More Info in  below.
From Kurli, crabs, which were present in droves in the vicinity of the original village. More info: Kurla
Lokmanya Tilak Terminus:
Originally named Kurla Terminus, it was renamed after freedom fighter Lokmanya Bal Gangadhar Tilak. More Info: Lokmanya Tilak Terminus
Named after the Mahalaxmi temple nearby. More Info: Mahalaxmi railway station
One of the original 7 islands that formed the ‘Island City’, also from ‘Mahikavati’ as it was called in the 13th Century CE. More Info: Mahim
Named after the Marine Battalion Lines that were housed here, later converted into Air Force Residences. More Info: Marine Lines
Naka means corner, junction. These days, also a crossroad. The name Marol comes from Morvol, as it was known during the Mahikavati era. More Info in  below.
The area around this station is known as Masjid Bunder, ie ‘Port with the Mosque’. The ‘Masjid’ does not mean a mosque as usually mentioned, but a synagogue dating from the times of Tipu Sultan, which was known as the Juni Mashid (Old Mosque). More Info: Masjid railway station
Matunga & Matunga Road:
One of the villages on the Mahim island. One source traces it to Matang, elephants, which means that around the time of ‘Mahikavati’, this was where the king’s elephants were housed. More Info in  below.
The Indian Government Mint in Mumbai was first established in 1829. Housing was provided to Mint staffers at the Mint Colony, and the road where it was based is known as Mint Road. More Info: India Government Mint, Mumbai
Originally a village named Mira, this area was converted into a township by amalgamating it and 4 other villages into a Municipal Council to support the growing infrastructure of the Mumbai Metropolitan region, and the station was named after the village. More Info: Mira Road
As per Wikipedia, the place finds its name listed as Mucchalind during the times of Chandragupta Maurya. However, no clearer source exists – and all other sources online list the Wiki article as the source.  below lists it as Mulund only, except pronounced differently. More Info: Mulund
Originally Bombay Central, short for Bombay Central Terminus, the terminus station from where long distance trains start/end on Western Railway. More Info: Mumbai Central railway station
Named after the erstwhile princely kingdom of Mysore, now the city of Mysore (now renamed Mysuru) and whose residents came from this part of the country. More Info: Google Maps
From Naur, or Naoor, during the Mahikavati era. Nau meant barber in Marathi, so probably referred to barbers in that time. More Info in  below.
Etymologically traceable to Surparaka, or Supraka, which was the name of the city – a capital city of the Aparanta empire – during Ashokan times. More Info: Nala Sopara
In the times of the Mahikavati kingdom, this area used to be the seat of justice for the king’s administration. Effectively, where the courts were situated. The judges – all Brahmins, the court administrators, staffers, etc. soon moved nearby and the village was born as Nyayagaon, the Village of Justice. This has been corrupted to Naigaon over the centuries. More Info: The Rise of Bombay: A Retrospect : Stephen Meredyth Edwardes : Free Download & Streaming : Internet Archive
Parel & Lower Parel:
Both named after one of the original 7 islands that formed the ‘Island City’, Parel. The word comes from either the paradi tree, a flowering plant that prospered in this area, or the Parali village, from where many residents originated and a temple was constructed in memory of the Lord resident there. More Info in  below.
Reay Road: Named after Donald James Mackay, 11th Lord Reay, who was the Governor of Bombay from 1885 until 1890. More Info: Reay Road railway station
Named after William Mansfield, 1st Viscount Sandhurst, who was the Governor of Bombay between 1895 and 1900. More Info: Sandhurst Road
Where the current Sacred Heart Church is, there used to be a Holy Cross and church well before the Marathas fought a war with the Portugese, won, and destroyed the church. The words for Holy Cross, Santa Cruz, became the de facto name of the area, and the railways made it one word, Santacruz, when naming the station servicing it. More Info: Santacruz, Mumbai
Mentioned as Sofale, it has been existing as a port town since 200 BC with the names Sefareh-el-Hind and Sefarah-el-Zing as the Konkan terminus of the trade with the African coast. Sefareh means journey/point of departure in Arabic, which is consistent with the idea that it was a port. More Info in  below.
Probably from Sivadi or Sivavadi, Garden of Shiva. More Info in  below.
When the Portugese took the islands of Bombay by force, they gave some part of this island to the Jesuits, who built a church there, dedicated to Mt. Zion. This area formed the boundary between the Porugese held and British held areas, hence the Marathi name, शीव Sheev (Boundary) while the Hindi & English names colloquialize Zion to Sion. More Info: Sion, Mumbai
The old name of the city seemed to be Sri Sthanaka, ‘Place of Lord Ganesha’, which got bastardized to Tanna by the Portugese and Thane by the British. More info: Thane
Named after freedom fighter Lokmanya Bal Gangadhar Tilak. More info: Bal Gangadhar Tilak
Mentioned as Intwally in the 1600s, (probably because of brick structures, int = brick) and later as Titvala. More Info in  below.
Ulhasnagar: Originally born as Kalyan Military Transit Camp, this area housed soldiers and war-related workers during World War II. Later, after Partition, those displaced from the Sindh province now in Pakistan were housed here, and it was converted into a full-fledged township. Ulhas means Joy, and the town was named Ulhasnagar by the then Governor-General of India, C Rajagopalachari. However, there is also an Ulhas River, which runs through the town, and some state that was the reason why the city is named so. More info: Ulhasnagar & Ulhas River
Named after the Vaitarna river that flows nearby, which itself is probably named after the Styx river of Indomythology, the Vaitarni, which acts as a boundary between the current lands of humans and the afterlife of heaven & hell. More Info: Vaitarna
Vasa Konkani (The name of the local residents back then) >> Baçaim (The name given by Portugese Settlers who built a fort there) >> Bassein (The British way of saying it) >> Vasai as it is known today. More Info: Bassein Fort
Was known as Vasi during the Mahikavati reign. More Info in  below.
The last station on the railway before an incline which took time to build, it was also known as Fulsheher, and Wasinda in the 1800s. More Info in  below.
The local language name is Vesave, which mean a place to rest for the weary. This was bastardized to Versova by the Portugese and the British. More Info: Versova, Mumbai
Between the stations of Ghatkopar & Kurla, came up one of the largest college campuses in the city, built by the Somaiya family. They named it Somaiya Vidyavihar, as it was a group of colleges rather than just one. Vidya = Knowledge, Vihar = Residence. Hence Vidyavihar = abode of knowledge. Over time, a need was felt to create a station to service students of these colleges, hence a new station was mooted, named Vidyavihar. More Info: Vidyavihar
Interesting eytmology here. Comes from Vikharvali or Vikhrauli circa 12th-15th Centuries CE. vali or -auli means a small village or a hamlet. Vikhar comes from विष, poison. So a poisoned hamlet, perhaps? More Info in  below.
Unlike the question of who came first, the chicken or the egg, Parle Products, and their first product, Parle G, named itself after the area that was named as per the local temple for the deity named Parleshwar. Another local temple deity, Vileshwar, donated the first half of the station’s name. More Info: Vile Parle
The local goddess is Jivdani Mata, a transmission from another goddess, Ekvira. Ekvira = Ek एक (One) + Veera वीरा (Brave), which means Brave Goddess. The Veer part part gave rise to the area, Virar. More Info: Jivdani Mata
VNP and RC Marg:
This monorail station is on the junction of two roads: VNP Road & RC Road. VNP is short for Vitthal Narayan Purav, who according to What is Full Form of V N Purav Marg of Chembur was a philanthropist who funded the construction of the road. RC is short for Ramkrishna Chemburkar, about whom I am not able to find anything yet. When I do, I’ll update the answer. More Info: Google Maps
Wadala, Wadala Bridge, Wadala Depot:
In all probability, from Vad, Banyan tree, and Ali, village, hence a banyan tree village. The bridge & depot are locations within the suburb where Monorail stations are built. More Info in  below.
Western Express Highway:
This Metro Station is right next to the Western Express Highway, one of the two arteries of the city that then connects to the Mumbai-Ahmedabad Highway. More Info: Google Maps
There are over 150 stations in Mumbai, covering the Western, Central, Harbour, Trans-Harbour etc. Railway lines, the Mumbai Metro & the Mumbai Monorail. I have, as of 3 Feb 2016 (nearly a year since my last edit), covered only 90 of them, just under the century mark. Will keep adding more as I get time, and I do hope to finish all of them.