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)
