I've never timed myself, but I'd have to say it's either Mass Effect 2, Panzer Dragoon Saga, or Halo Combat Evolved. ALl for different reasons.
I had to replay large portions of Mass Effect 2 trying different senarios trying to get both Maranda and Jack to be loyal and keep everyone alive in the end.
Panzer Dragoon Saga is my all time favorite RPG and I've replayed it more than any game. It's not the longest game if you just do the story, but it takes longer to get all extras and fully level up your Dragon.
Out of all the Halo games I've replayed the first the most. Plus I spend countless hours playing LAN with friends. I never really got into online play much so while I've played multiplayer in them all I think I've spent the most time playing the first.
Donkey Kong arcade may start ranking high on my top played list since I've been trying to get a respectible score on my arcade cabinet. I'll never beat Bill, Steve, or the Doc, but I would like to beat that little toad Brian Kuh.