I've done several Halo 3 play throughs mostly to help other people with the legendary difficulty because well, for some strange reason even though I should know better I really enjoy playing the storyline.

I've repeated most of the MW2 spec ops missions multiple times. I would say however the biggest replayed game aside from an FF game is probably Front Mission 3 which I replayed 4 times originally because of different story line outcomes and other than that I've now done like 4 play throughs of Dragon Age Origins but ultimately I think it has to go to Ace Combat 4 and Ace Combat 6 I've played the stories of those games so many times I know exactly how to approach each mission by name alone.