Child of Light-Vita/Steam
Rayman Legends same as above
Final Fantasy X HD-Vita/Ps3/Steam
Final Fantasy Psx trilogy-Ps store/Steam
Several assassin's creed on ps3/steam

There's probably more but those are the ones I can think of right now

So it seems. Most MGS games seem to be cheap overall except for the PC versions, Twin Snakes, Ghost Babel and the MSX games.

Digimon World Dusk - the first one i bought online and it turned out to be a counterfeit copy which Nintendo has blocked from working on 3DS consoles, so i bought a legit copy. then i lost that legit copy after selling away the counterfeit one. now i emulate it on my tablet.

Pokemon Ranger - bought 2 copies. lost the first and sold the second.

Pokemon Platinum - same situation as DWD, first one was a counterfeit so i bought a legit one. i still have both.

Mario Kart 7 - bought the physical copy. hated it. lost it. then i got again digitally when Club Nintendo died. i still hate it.

Minecraft - bought the Java version and received the Win10 version for free.

Metroid Prime Trilogy - recieved it as a gift when i was a kid. i didnt like it very much so i sold it and then later bought it digitally on Wii U.

Super Mario Bros - i own it on both the Wii U and 3DS virtual console.

Terraria - PC and XBox 360 versions. i got the 360 version for free.

Sunset Overdrive - got the game through GWG but then my membership expired. i then bought a used copy for $10

Rayman Origins - i got the Wii version, and then later wanted to replay it in HD so i bought the PC version.

Rayman Legends - bought the Wii U version and then got the XBONE version for free.

Spore - yes. i bought this twice. no regrets.

World of Goo - i bought the WiiWare version many years ago and then wanted it on PC, so i got it again.

Human Resource Machine - same with WoG, only i have another unused PC code from Humble Bundle

Stardew Valley - bought a copy and then got another copy through Humble Bundle, so i gave it to a friend

Various Saints Row games for various reasons im not even sure of at this point

Various versions of Pac-Man across various platforms.

and others than i dont even care enough to remember

Alan Wake. Standard Edition and Limited Edition
Gears of War 2. Standard Edition and Game of the Year Edition. I regret that later purchase.

Let's see.

A lot of games via virtual console and compilations like Rare Replay, Sonic's Ultimate Genesis Collection, etc.

Ocarina of Time four times: N64, GCN Collector's Edition, GCN Master Quest, Ocarina 3D
Majora's Mask twice: N64 and 3DS
Twilight Princess three times: GCN, Wii, WiiU
Wind Waker twice: GCN and WiiU
Ico and Shadow of the Colossus twice: PS2 and PS3
Halo twice: Xbox and X360
Retro City Rampage twice: PSV and PS4
Star Fox 64: N64 and 3DS
Half-Life 2: Xbox and X360

That's all I can think of now.

College Hoops: NCAA 2K7 (PS2/PS3)
Crash Nitro Kart (PS2/XB)
Dead Rising (360/PS4)
Disney Tangled (DS/Wii)
Fantastic Four (PS2/GC)
Fantastic Four: Rise of the Silver Surfer (PS3/Wii)
Final Fantasy X/X-2 (PS2/PS3/PS4)
God of War: Ghost of Sparta (PSP/PS3 Origins version)
Guitar Hero III: Legends of Rock (Wii/PS3)
Half-Life 2 (XB/360 Orange Box version)
The Legend of Zelda: Ocarina of Time (N64/3DS)
The Legend of Zelda: Majora's Mask (N64/3DS)
Metal Gear Solid 2 (PS2 Sons of Liberty version/XB/PS3 HD Collection version)
Metal Gear Solid 3(PS2 Snake Eater version/PS3 HD Collection version)
Minority Report: Everybody Runs (PS2/XB)
MLB 08: The Show (PS2/PS3)
NHL 07 (PS2/PSP)
NHL 08 (PS2/PS3)
Ninja Gaiden (XB Black version/PS3)
Ninja Gaiden 3 (PS3 original version/WiiU)
Prince of Persia: Warrior Within (GC/PS3 Trilogy version)
Ready 2 Rumble Boxing (PS1/N64)
Sonic the Hedgehog (GEN/GC Mega Collection version)
Sonic the Hedgehog 2 (GEN/GC Mega Collection version)
Sonic Spinball (GEN/GC Mega Collection version)
Spider-Man 3 (PS3/Wii)
Street Fighter II (GEN Special Champion Edition version/SNES original version/PS2 Capcom Classic Collection version/PSP Capcom Classics Collection Reloaded version)
Street Fighter IV (PS3 original version/PS3 Arcade version/PS3 Ultra version)
Super Mario Maker (3DS/WiiU)
Super Smash Bros. (3DS/WiiU)
Tekken Tag Tournament (PS2/PS3 Hybrid version)
Tekken 5 (PS2/PSP)
TNA Impact (PS2/PS3)
Tom Clancy's Spinter Cell: Double Agent (PS2/360/PS3)
Tony Hawk's Pro Skater 3 (PS1/GC)
WCW Mayhem (PS1/N64)
Wheel of Fortune (NES/GEN)
WWF War Zone (PS1/N64)
WWE Smackdown! vs. Raw 2006 (PS2/PSP)
WWE Smackdown vs. Raw 2007 (PS2/PSP)
WWE Smackdown vs. Raw 2008 (PS3/Wii)
WWE Smackdown vs. Raw 2009 (PSP/PS3)

Fallout 3 - Own boxed PC version, a steam copy of the GotY Edition, and a sealed collectors edition on X360

Mass Effect Trilogy - Own the individual games on X360, and the trilogy collection on PS3

Assassin's Creed 4 - Have a disc on Wii U, and a digital download on PS4

Red Dead Redemption - Have discs on both X360 and PS3

Final Fantasy III - For some reason I have two of these on Famicom, I don't remember why.

Dead Space - Have boxed on PS3 and Steam

Spec Ops the Line - Have boxed on PS3 and Steam

Xcom Enemy Unknown - Have boxed on PS3 and Steam

Dragon Age Origins - Have a download on PS3 and a PC disc

Super Mario Bros 3 - Have on Wii VC and a boxed Famicom copy

F-Zero Maximum Velocity - Have a cart on GBA and a download on 3DS

Halo: Combat Evolved - Got two Xbox copies, one is GotY and the other is OG

Need For Speed Most Wanted - Got on both Xbox and GameCube

The Orange Box - Got the disc on X360 and all the games included on Steam

Star Wars KOTOR 1&2 - Got on Xbox and Steam

Star Wars Jedi Academy - Got a PC disc and on Steam

Star Wars: Jedi Outcast - Got a PC disc and on Steam

Star Wars: Republic Commando - Got on Xbox and Steam

Star Wars: Battlefront 2 - Got on Xbox and Steam

Star Wars: Rogue Squadron - Got two N64 carts for some reason

Think thats all of them

Oh gosh. I'm notorious for this

Ratchet and Clank 1-3
Jak 1-3
Sly 1-3
God of War 1-3
Skyrim
Heavy Rain
Beyond 2 Souls
Uncharted 1-3
Crash 1-3
Crash Team Racing
Psychonauts
Spiderman 1 and 2 (the old PS1 versions)
The Last of Us

TWD Season 1

Journey

Flower

and more I'm forgetting I'm sure

The Wind Waker + HD

and Tales of Symphonia + Chronicles

Minecraft ( Wii U / PC)
Hyrule Warriors ( Wii U / 3DS)
Super Smash (Wii U / 3DS)
Sims 3 ( Wii / PC)