Among games that actually track hours... the only one I've gone over 100 in is Fallout: New Vegas, at 558 hours currently.
But I've definitely played City of Heroes more than that, considering I played from 2004 to 2008 and still play sporadically (though I can no longer access all of my 60+ toons >.< )
So it's
1-City of Heroes/Villains
2-Fallout: New Vegas
3- ...err... probably Chrono Trigger, considering how many times and on how many different platforms I've gotten all of the endings. Then again, in Final Fantasy Tactics(War of the Lions) I've maxed a few characters out before... I've also put a whole lot of time into Gran Turismo 5, though I'm not certain if it compares...
I suppose number three is unknowable.