I don't know, im not the one to replay games, usually try to get everything/spend as much time as possible in the game so that i can leave it alone after finishing it, probably it would be .hack//G.U. Rebirthm, beat it like 5 times, very rarely beat a game more than once, the only others i can rember are Persona 3, like 3 times, GTA SA, Megaman Zero and batman returns on the snes? maybe, don't remember if i beat it the 2nd time

If you count shorter games that you can beat in an hour or so, then Starfox on SNES.
Must have beaten it nearly a thousand times over the years. (It was the first video game I ever got, in 1994)

Metal Gear Solid 4, Metal Slug (X, 4, 5), Sonic The hedgehog, Altered Beast. I'm not including fighting games because usually you do an arcade run in 30min, so KOF, SSB, Tekken and others would skyrocket on the list.

Pokemon Blue/Yellow is the only game I have played more than two times....

I think that this things invalidate the replay count. I loved Persona 4, but it's an 80 hour game and I simply can't finish it more times than games with 8 hours. Counting old games that could be beaten in less than an hour then...

Uncharted 3 about 5 times or so. Wait no Ratchet and Clank UYA 11 times at least. MGS3 at least 5 times. I replay most of my permanent games pretty regularly. All the Jak games a few times. Resistance 3 a few times. Batman Arkham games at least 5 times.

Probably Castlevania. I've beaten it in either the hundreds or the thousands.  There are times I've beaten the game several times in one sitting. I can finish it in around 15 minutes.

Oracle of Ages - around 35 times
Oracle of seasons - around 20 times
Pokemon Gold - 250+ Hours
Pokemon X - 130+ Hours (There are some afk breeding here though)
Skyrim - 100+ Hours
Mario Kart 64
Smash 64
Goldeneye 64
Starfox 64
Ocarina of time - Around 5 times


Damn, now i have to find my 64 again...

@Edit
Sorry, didn't read the full title. Took Chrono trigger out of the list.

Final Fantasy X.

Gears of War 2, like more than 20 times.