Virtual Cop 2 (PC) - 10 times.
Beyond good and evil (PC) - 5 Times.
Mafia the city of lost heaven (PC) - 4 Times.

Please update all responses with platform played on and then reply to this reply letting me know you've done so, then I will add these. Thanks!

I'll give this a go.

Final Fantasy (Once on the NES and once on PS1 on the Origins compilation)
Legend of Zelda (12 on NES, twice on Wii U VC)
Super Mario Brothers (100+ times on NES)
Super Mario Brothers 3 (75+ times on NES)
Super Mario World (50+ times on SNES)
Mario 64 (12+ times on N64, 1x on DS/3DS) (100% 2 saves)
A Link to the Past (5 on SNES)
Final Fantasy VI (8 times on SNES, 2x on GBA, 2x on PS1, 1x on PS3, 1x on PSVita)
Final Fantasy VII (1x on PS1, 1x on PSVita)
Xenogears (1x on PS1, 1x on PSVita)
Chrono Trigger (13 times on SNES, 1x on DS, 1x on PS1, 1x on PSVita)
Secret of Mana (3x SNES)
Turtles in Time (12+ times SNES)
Mega Man X (5x on SNES)
Diablo (PS1, 2x)
Diablo 2 (PC, at least 20 times)
Diablo 3 (PS4, 7 times)
Mass Effect (X360 4 times, PS3 once) (100% on X360)
Mass Effect 2 (X360 3 times, PS3 once) (100% on X360)
Mass Effect 3 (X360 3 times, PS3 once) (100% on X360)
Bioshock (X360 twice, PS3 once) (100% on X360)
Bioshock Infinite (PS3 3 times) (100%)
Catherine (PS3 twice)
inFamous (PS3 twice) (100%)
inFamous 2 (PS3 twice) (100%)
inFamous Second Son (PS4 twice) (100%)
Injustice Gods Among Us (PS3 twice, PS4 once)
Batman Arkham Asylum (X360 twice, PS3 once)
Batman Arkham Origins (PS3 twice)
Mafia 2 (X360 once, PS3 once)
Dead Space (X360 once, PS3 once)
Dantes Inferno (PS3 twice) (100%)
Marvel Ultimate Alliance 2 (5x PS3) (100%)
Mortal Kombat vs DC Universe (2x X360 1x PS3)
Resident Evil 5 (3x X360) (100%)
Fire Emblem Awakening (2x 3DS)

Edit: Thought of a couple more.

Shining Force (Genesis, 4x)
Shining Force 2 (Genesis, 2x)
Popful Mail (Sega CD, 4x)

Lion king Sega Megadrive- 2 times
Sonic 1 Megadrive- 2 times
sonic 2 Megadrive-2 times
Shining Force Megadrive&GBA-3 times
Shining force 2 Megadrive- 2 times
Advance wars GBA-7 times( once hard mode six normal) 100%
Advance wars 2: Black Hole Rising GBA-6 times( twice hard mode four times normal) 100%
Fire emblem GBA- 2 times
Fire emblem The Sacred Stones GBA- 3 times 100%
Pokemon Sapphire GBA- 5 times
Pokemon Ruby GBA- 3 times
Pokemon Emerald GBA-2 times
Pokemon Fire Red GBA- 2 times
Pokemon Leaf Green GBA- 2 times
Kingdom hearts 1/FM PS2&3- 2 times
kingdom hearts 2/FM PS2&3- 2 times
Kingdom Hearts: Chain of Memories/REcom PS3&GBA - 4 times(three times on gba once on ps3)
Kingdom Hearts Birth by Sleep/FM PS3&PSP- 2 times
The Wolf Among Us PS3-4 times100%
Command & Conquer PS1&PC- 4 times(twice on each)
Command & Conquer Tiberian Sun PC-2 times
Command & Conquer Red Alert PS1&PC- 4 times (twice on each)
Command & Conquer: Red Alert 2 PC- 2 times
Dust: An Elysian Tail PC&Xbox 360-2 times
Borderlands Xbox 360- 2 times
Borderlands 2- Xbox 360-2 times
Tales of Vesperia Xbox 360-2 times
Lost odyssey Xbox 360-2 times
Blue dragon Xbox 360-2 times
fable The lost chapetrs Xbox-2 times
Fable 2 Xbox 360-2 times
Fable 3 Xbox 360-2 times
Halo 3 Xbox 360-2 times
Halo 3 odst Xbox 360-2 times
Halo Wars Xbox 360-3 times
Gears of War Xbox 360- 2 times
Gears of War 2 Xbox 360-2 times
Castle Crashers Xbox 360- 3 times

I can't remember many exact numbers so these are all conservative estimates (really)

NES

Adventures of Lolo - 5 times
Contra - 3 times
Double Dragon - 3 times
Double Dragon II - 3 times
Dragon Warrior - 2 times
Duck Tales - 3 times
Final Fantasy - 20 times
Kirby's Adventure - 5 times
Mega Man - 3 times
Mega Man 2 - 20 times
Mega Man 3 - 10 times
Mega Man 4 - 5 times
Mega Man 5 - 10 times
Mega Man 6 - 3 times
Super Mario Bros. - 10 times
Super Mario Bros. 3 - 20 times

SNES

Chrono Trigger - 10 times
Contra III - 3 times
Donkey Kong Country 2 - 3 times
EarthBound - 3 times
Final Fantasy IV - 3 times
Final Fantasy V - 2 times
Final Fantasy VI - 3 times
Lufia II - 2 times
Mega Man X - 10 times
Mega Man X2 - 5 times
Mega Man X3 - 5 times
Super Mario World - 5 times

Genesis / Mega Drive

Contra: Hard Corps - 20 times
Dynamite Headdy - 10 times
Golden Axe - 3 times
Golden Axe II - 2 times
Gunstar Heroes - 3 times
Ranger X - 10 times
Sonic the Hedgehog 2 - 30 times
Streets of Rage II - 5 times
ToeJam & Earl - 3 times

Dreamcast

Ikaruga - 10 times

PS2

God of War - 5 times
God of War II - 3 times
Grand Theft Auto: San Andreas - 4 times
Silent Hill 2 - 10 times
Silent Hill 3 - 3 times
Twisted Metal: Black - 15 times

Xbox 360

Super Meat Boy - 6 times ( 106% completion )

PC

Half-Life - 10 times
Half-Life 2 - 10 times

Mega Man 2 - 8 times
Mega Man 3 - 4 times
Mega Man 4 - 6 times
Castlevania II: Simon's Quest - 24 times

I used to speed run Simon's Quest which is why I have so many playthroughs.

*NES for all

I've played Metroid Fusion so many times since it launched. I probably passed 100 playthroughs a long time ago but we'll go with 85 just to be safe, lol.

The original Super Mario Bros, at least 100 times.

Tales of Symphonia (GCN) 5 times, on 6th run
The Wind Waker 3 times (2 original, 1 HD)
Harvest Moon Island of Happiness (DS) 3 Times
Fire Emblem Awakening (3DS) 3 times (Normal, Hard, Lunatic)
Fire Emblem Sacred Stones (GBA) 3 times (both routes, 3rd Ephriam)
...

There is a lot of games I beat twice and I have trouble remembering them so I'll leave those out

Please edit with what devices you played these games in, then reply to this to let me know. Thanks!