I tried doing this last year, and got enough responses to compile a short list, which I broke down roughly by generation that the systems belonged to. Here's the thread, if it's useful:
http://cheapassgamer.com/forums/showthread.php?t=112973
And the list, snipped from that thread:
[quote name='bookishboy']8-Bit Era (and earlier)
-Double Dragon (NES was 1player game, Sega Master System was a port of this game but added 2player co-op)
16-Bit Era (SNES/Genesis)
-Aladdin (SNES and Genesis were different games)
-Beavis and Butthead (SNES was side-scrolling, Genesis was adventure game)
-Dragon's Lair (SNES game was a side-scroller, arcade title was animated clips streaming from a laserdisc. SNES version seems to have had some [?] animated cut-scenes thrown in though)
-MoonWalker (Genesis was sidescroller, arcade version was overhead view)
-Mortal Kombat (SNES version lacks blood, less violent finishing moves than Genesis)
-Pagemaster (SNES and Genesis versions were both platformers but with different gameplay mechanics; SNES had a jump attack, Genesis had a weapon attack)
-Samurai Showdown (SNES has character Earthquake, Genesis has characters who change size to reflect scale/distance,...3DO and Sega3D also different?)
-Scooby-Doo Mystery (SNES and Genesis versions differed, SNES was platform[?] and Genesis was adventure[?])
-Shadow Dancer (Genesis was different from Arcade title)
-Shadow of the Beast (SNES version was ported from Amiga, made easier)
-ShadowRun (SNES was point-and-click RPG-ish, isometric view. Genesis version was top-down and action-oriented)
-Sparkster (SNES and Genesis were different games)
-Spider-Man (Genesis had 2 games with the same name but which were different games. One is referred to as "The Animated Series" and the other one was re-released as "The Amazing Spider-Man vs. The Kingpin" on SegaCD)
-Strider (Genesis was different from Arcade title)
32/64-Bit Era(PS1/Saturn/N64)
-Marvel Super Heroes vs SF (Saturn had tag-team, PS1 did not)
-Marvel vs Capcom (DC had tag-team, PS1 did not)
-X-men vs Street Fighter (Saturn had tag-team, PS1 did not)
PS2/GC/XBox and newer
-Call of Duty 2 (XB360 and PC were one game, GC/PS2/XB each were ports of the other, and subtitled "Big Red One")
-FarCry (XB version subtitled "Instincts" was different story from PC version. XB360 version, "FarCry Instincts Predator" included entire XB version plus an additional chapter/story)
-Ghost Recon 2 (XB and PS2 were different games)
-Madden 06 (XB360 different from the PS2/XB/GC versions)
-MotoGP (PS2 and XB were different games)
-Spiderman 2 (PC version different[and sucky?] from XB/PS2/GC)
-Splinter Cell: Double Agent (XB360 version different story? from PS2/XB/GC)[/quote]
Cheers