I think the game that I have beaten the most is Final Fantasy VIII with about 15 complete playthroughs. Super Mario World 3 on the NES is probably pretty close behind.
I'm thinking Bayonetta is gonna be added to my list. I replayed it again recently before I knew B1 was coming to WiiU, and I'm for sure gonna play it at least on easy mode to make use of her cool Nintendo costumes. It'll make 4 times. I don't replay much D: