Well, in terms of my recent gaming, I've put in at least 200-250 hours in Persona 3 FES, which is a lot considering I've had it for less than a year (for me it is, anyway).
However, *the* game I've played for the longest amount of time is almost certainly Harvest Moon 64. When I was 10, I got my mother to rent it so often that she speculates (and could well be right) that she paid the full price of the game once or twice in rental fees before getting tired of it and simply buying it for me. Days upon days of playing the game, then leaving it for a while, then starting a new file...
I have no idea how many hours I've spent on it, as I've had it for a very long time, but it's still my most played game.