Lets see...
Timesplitters Future Perfect: 2 copies - 1 xbox, 1 PS2
Timesplitters 2: 2 copies - 1 gamecube, 1 PS2
Okami: 2 copies - 1 PS2, 1 Wii
COD4: 2 copies - 1 360, 1 PS3
Orange Box: 2 copies - 1 360, 1 PS3
Left 4 Dead: 2 copies - 1 360, 1 PC
Left 4 Dead 2: 2 copies - 1 360, 1 PC
Modern Warfare 2: 2 copies - 1 360, 1 PS3
Bad Company 2: 2 copies - 1 360, 1 PS3
Fable: 2 copies (If you count Fable and Fable: The Lost Chapters as the same game) - both on xbox
Halo 2: 2 copies - 1 PC, 1 xbox
Unreal Tournament 3: 2 copies - 1 PC, 1 PS3
Mass Effect: 2 copies - 1 360, 1 PC
Mass Effect 2: 2 copies - 1 360, 1 PC
Marvel vs. Capcom 2: 2 copies - 1 Dreamcast, 1 XBL Arcade (yeah, still have my dreamcast version)
Power Stone series: 2 - both games on Dreamcast, both on one disk on PSP
Pokemon Silver: 2 copies - GBA, DS
Phantasy Star Online: 2 copies - 1 Dreamcast, 1 Gamecube
Beyond Good and Evil: 2 copies - 1 xbox, 1 PC (Damn microsoft for not making it backwards compatible...)
And thats all I can think of.