This map shows all railways that have been operated by Palestine Railways, Israel Railways, or have existed on the territory of Israel/Palestine.
Certain sources show more train stations at:

Nevatim (31°13′0.12″N 34°52′34.48″E﻿ / ﻿31.2167°N 34.8762444°E﻿ / 31.2167; 34.8762444),
Dvir (31°24′52.94″N 34°47′38.95″E﻿ / ﻿31.4147056°N 34.7941528°E﻿ / 31.4147056; 34.7941528),
Nuseirat (31°27′26.00″N 34°24′31.12″E﻿ / ﻿31.4572222°N 34.4086444°E﻿ / 31.4572222; 34.4086444),
Zarnuqa (31°52′32.19″N 34°45′48.99″E﻿ / ﻿31.8756083°N 34.7636083°E﻿ / 31.8756083; 34.7636083),
Tirat al-Lawz (32°45′25.02″N 34°57′33.28″E﻿ / ﻿32.75695°N 34.9592444°E﻿ / 32.75695; 34.9592444),
Kabara (32°34′17.27″N 34°56′8.87″E﻿ / ﻿32.5714639°N 34.9357972°E﻿ / 32.5714639; 34.9357972),
and a few east of Haifa.I could not find a secondary source, and so they have been left out. There might also have been a Haifa-Wadi Rushmiya line. The station at Birein was probably more of a simple water refilling stop; this is possibly the same for other former stops in the Negev.
The J'slm - El Bireh line was a military railway built by the British in 1918 to supply the war front North of Jerusalem. Very little information is available on it, and so its path is very hypothetical; this is also true for other lines (mostly in the Negev).
Names: I tried to put former names where possible (space permitting). A plethora of translations, transliterations, and transcriptions exist when romanising Hebrew and Arabic station names. Since this map is in English, I have preferred the name that appeared the most "English" in my eyes. For clarity, a hyphen "-" is used to separate the town name from a qualifier.

Borders:   Undisputed borders   1949 Green line   1974 Purple line   East Jerusalem municipal borders
Train Lines:   Open (electrified)   Open   Open (freight only)   Being built   Closed
The background map is a merger of Israel location map.svg and Egypt location map.svg, both by NordNordWest, and also licensed under CC-BY-SA-3.0.
Palestine Before The 1948 Nakbah, Dar Al Maalem, 2008. (available here: http://www.palestineremembered.com/Acre/Maps/Story11857.html).
Palestine, Survey of Palestine, August 1944. (available here: http://www.palestineremembered.com/Acre/Maps/Story582.html).
Palestine, British War Office, 1924. (available here: http://upload.wikimedia.org/wikipedia/commons/b/b6/Palestine_north_1924.jpg and http://upload.wikimedia.org/wikipedia/commons/b/b8/Palestine_south_1924.jpg).
Map of Israel, Boris Chomenko, 2010. (available here: http://www.bueker.net/trainspotting/map.php?file=maps/israel--palestine/israel--palestine.gif).
Google Maps (https://maps.google.fr/?ll=31.587894,35.606689&amp;z=7) for the realignment of the Beersheba railway, Jaffa-Jerusalem Railway, and the Yavne-Ashdod extension.
Topomapper (http://www.topomapper.com/index.html?zoom=7&amp;lat=31.69431&amp;lon=35.01648) for the Rafah-Kantara line (this link is now dead, but the website vlasenko.net publishes the same source material).
This page (http://www.rail.co.il/EN/Stations/Pages/israelrailways-station_index.aspx) for the current passenger service.
This page (http://www.rail.co.il/HE/Development/Pages/מפתתוכניתהפיתוח.aspx) for the future passenger service.
Rakevethaemek_map_eng.png by en:User:Ynhockey for the location of stations along the Jezreel Valley Railway.
A1 railway.png by en:User:Ynhockey for the route of the Jerusalem high-speed railway.
This map (http://www.port2port.co.il/ViewImage.asp?CategoryID=336&amp;ArticleID=71338) for the Railway to Karmiel.
This page and its map (http://www.rail.co.il/HE/Development/Executed/Pages/AshqelonBeerSheva.aspx) for the Ashkelon-Beersheba railway.
This map (http://en.wikipedia.org/wiki/File:רכבת_העמק.jpg) for the new Jezreel Valley Railway.
This flickr album (https://www.flickr.com/photos/39631091@N03/sets/72157625896029333/with/8064048522/), which was an invaluable source for the Afula-Nablus-Eastern railway-Lod-Beersheba-Birein route.
Hebrew Wikipedia articles: he:המסילה המזרחית, he:רכבת העמק, he:הקו הראשי של רכבת ישראל, he:מסילת השומרון.
Pretty much anything else I could get my hands on.
Mapeh