Mine was metroid prime. I beat it 17 times and got 100% 10 times. My second is pokemon red . I beat that 13 times and all of the pokemon 3 times.

Paper Mario
about 18 times
good game

Almost surely Golden Axe on the PC. I probably finished it at the very least 10 times when I was young. Maybe more than 20.

Have beaten Wow 3 times so far ( killed Illidan 3 times lol).

By the time the next patch comes I should have beaten it like a dozen times ! 1 time a week !

Hmm... I'm sure I've beaten Turtles in Time in excess of 25 times...

Super Mario World must be right up there as well.

I beat Baldur's Gate 2 something like 3-5 times, and started numerous other games that I never finished. Might not sound like much, but the game is easily 30+ hours long.

Aside from that urmm.. I've beat Halo 2 five or six times, but that was mostly playing the co-op with a variety of friends. I don't even like it that much, but haven't got any better co-op shooters. =P

Uncountable games of Master of Orion 1/2/3, Civilization 2, various Total War games etc, but nothing else that I can give proper numbers on.

its probably RE4 which i have beat over 25 times

omg - ever hear of buying a new game? i think super mario world is my most beaten game and that was like 4 or 5 times.

Well at the moment I'm working my way through Ghost Squad. I suppose I've finished it about 30 times already.

If you are after a more lengthy game, I finished Chrono Trigger to all 13 endings, though I wouldn't have done this without an emulator. First time through the game was maybe 20 hours. 2-13th endings were all done on a second pass with save states and speedup, so it only took about 6 hours to do them all.

I really don't play games through that many times (or to 100%). I'd prefer to have experienced a large array of games, rather than only a few in significant detail.

Oh right, Ghost Squad.  I've finished that dozens of times as well.

I've also seen every ending (and every variation of every ending) for Chrono Trigger, original cartridge-style.  That must be around 20 times or so...