Demons Souls (PS3) 10 Times (100%)
Bloodborne (PS4) 8 Times (100%)
Zone of the Enders; The Second Runner (PS2) 12 Times (100%)

in the case of ZOE i beated the game 9 times on the PS2 and 3 times on the PS3 (thanks to the HD version since i lost my PS2 version when i lend it to a friend)

Halo 3 (360) - about 10 times on legendary. (I think it was more, but at least 10)

Sonic Generations (360) - 3 times 100%.

The Legend of Zelda: Ocarina of Time 3D (3DS)-6 times (100% twice)
Fire Emblem: Awakening (3DS)-2 times
Kid Icarus: Uprising (3DS)-3 times
The Legend of Zelda: A Link Between Worlds (3DS)-2 times (100% once)
Xenoblade Chronicles (Wii)-2 times, 3 if you count NG+ (100% once)
Pokemon Yellow (GB)-At least 5 times
The Legend of Zelda: Twilight Princess (Wii)-4 times
The Legend of Zelda: Skyward Sword (Wii)-3 times (100% once)
Paper Mario (N64)-3 times

I play most of the games I love multiple times. Sometimes, I play games way too many times. A few of these are rough approximations.

Final Fantasy IV (SNES/PS1): 3 times.
Final Fantasy VI (SNES/PS1): 5 times -- I don't know why. I hate this game. (100% once).
Final Fantasy VII (PS1/PC): At least 15 times. (100% at least 10 times.)
Final Fantasy VIII (PS1/PC): At least 12 times. (100% about 10 times.)
Final Fantasy IX (PS1): At least 12 times. (99.8% about 10 times. Never got Excalibur II.)
Final Fantasy X (PS2): 6 times. (Stupid Celestial Weapons. :( )
Final Fantasy X-2 (PS2): 3 times. (100% once.)
Final Fantasy XII (PS2): 3 times.
Final Fantasy Tactics: 2 times -- once PS1 version and once iOS version.
Chrono Trigger (SNES/PS1): 3 times. (100% once.)
Xenogears (PS1): 3 times. (100% once).
Spyro: Year of the Dragon (PS2): 3 times. (100% once.)
Jak 3 (PS2): 3 times.
Ratchet & Clank (PS2): 4 times. (100% once.)
Ratchet & Clank: Going Commando (PS2): 6 times. (100% once.)
Ratchet & Clank: Up Your Arsenal (PS2): 5 times. (100% once.)
The Last of Us (PS4): 2 times.
Valkyria Chronicles: 2 times -- once PS3 and once PC.
Starcraft II: Wings of Liberty (PC) -- Beat the campaign five times on normal, hard, and brutal difficulties.
Portal (PC): 2 times. (100% all times.)
Portal 2 (PC): 3 times. (100% all times.)
Mass Effect: 2 times on PC and once on 360. (100% once.)
Mass Effect 2 (PC): 3 times. (100% once.)
Curse of Monkey Island (PC): 3 times. (100% all times on Mega Monkey difficulty.)
Escape from Monkey Island (PC): 3 times. (100% all times.)
Tales of Monkey Island (PC): 3 times. (100% all times.)
Persona 4: 2 times on PS2 and 2 times on Vita.
Dangan Ronpa: Trigger Happy Havoc (Vita): 2 times.

Transistor (PS4): 2 times. (100% and Platinum'd.)

Dark Cloud 2 (PS2): 5 times. (100% two times.)

Ocarina of time on n64 x2
The curse of monkey island on PC x4
Goldeneye 007 on n64 x4
eldar scrolls oblivion on 360 x2
Fallout 3 on PC x2

That's all I can remember for now

I've beaten Pokemon crystal 5 times.

Pokemon Fire red  5 times

Pokemon Blue 3 times

Pokemon Emerald 3 times

I think that's about it. I dislike replaying games.

I'm too lazy to list all games, but I beat Pokemon Ruby about 8 times.

If we count ssb64 classic mode.....
I've cleared it with every single character multiple times. Well over 36 times for sure. but I'll go with 36.

SSB64 (N64) Classic Mode 36 times.

I'm not good at remembering such things but there are some exceptions...

Crysis Warhead - 6 times (PC)
Dishonored - 4 times (PC)
Fire Emblem: Radiant Dawn - 4 times (Wii)
Fire Emblem: Path of Radiance - 2 times (GC)

Man, my brother should use his account to post in this thread. He beat Okami like 15 times ^^

Should be said that R&C is basically made to be replayed.