Half Life (pc, ps2 and a pirate copy on Dreamcast (never officially released))
Fallout 3 (ps3, 360 and pc)
Fallout 4 (ps4, pc and xbone)
Skyrim (360 standard, pc, ps4)
Fallout New Vegas (ps3, 360 and pc)
Mario 64 (N64, DS)
Zelda Ocarina of Time (N64, 3DS plus gamecube bonus disc)
Zelda Windwaker (Gamecube, wii u)
Black (ps2, xbox)
Grand Theft Auto 5 (ps3, ps4)
Halo (xbox, pc)
Timesplitters 2 (ps2, xbox)
Oblivion (360, ps3)

Lots more to be honest. Mostly I get second version when its cheap.

Every Zelda game that was released more than once, Mario 3, Mario 64, Yoshi's Island, Star Fox 64, Knights of the Old Republic.

Mass Effect trilogy (Xbox 360 and PS3)
Sleeping dogs (PS3 and Xbox one)
Grand theft auto v (PS3 and Xbox one)
Star Wars: tfu (PS3, Xbox 360 and Xbox one)
Gears of war (remastered) (Xbox 360 and Xbox one)

uncharted collection (PS3 and PS4)

the last of us (PS3 and PS4)

halo trilogy and halo collection (Xbox-xbox 360 and Xbox one)

See ya soon there

For me the original Ratchet trilogy on PS2 and later PS3

A lot of the multi releases for pokemon mainline and mystery dungeon.

Sonic Unleashed on Wii and then PS3

Sonic and the Secret Rings on Wii twice

Injustice Gods Among Us first on Vita and then PS4

I think the only game i have actually owned twice is F-Zero X (N64 then Virtual Console)

Ratchet and Clank original trilogy (PS2, PS2 again, then PS3)

Kingdom Hearts 1 and 2. (PS2/PS3)

Star Wars Battlefront 2 (PS2)

Tony Hawk Pro Skater 3

Tony Hawk Underground 2
there are more, i just can't think of them right now.

Hm... off the top of my head: (I sometimes include remakes sometimes not lol)

- Twilight Princess (GCN, Wii and Wii U)
- Ocarina of Time (N64, Wii and 3ds)
- Majora's Mask (N64, Wii and 3ds)
- Breath of the Wild (Wii U and SW)

- Metal Gear Solid (PS1, PS3)
- Metal Gear Solid 2 (PS2, Xbox, PS3)
- Metal Gear Solid 3 (PS2, PS3)

And probably a lot more which I can't think of right now.

Skyrim - PS3 and PC
VVVVV - 3DS and PC
and quite a bit of virtual console games. Other than that I've actually managed to stay away from doing this all that much. Got to copies of tearaway with my vita as well, but I didn't buy it for those so I won't say those count. :P

Oh no! Someone else found my super secret Xbox version of MGS2, I'm going to have to go looking for the Windows PC version now to restore my broken self-esteem

You'd be surprised lol, only reason I got it is to have something else for my Xbox besides Shenmue II. The game was just 2€ anyways, guess demand for MGS2 "Xbox" is rather low. :P