Tough to guess.
This gen so far it has been LoZ:TP with about 180hours, but closely followed by RE4:Wii with about 10-20 hours less.
For the GC I played Timesplitters 2 for about 160 hours [so already passed by two Wii games 
]. I am not sure whether I spent more or less time on Windwaker though, I suspect a bit more [still less than 200hours I'm sure]
I have absolutely no idea how much time I spent on various N64 games... I imagine whichever game I played the most is over 200 hours though, but not hugely.
contenders for that would be Goldeneye or F1WorldGP2, possibly Pilotwings [it's hard to tell how much time passes with that one]
The only N64 title I can vaguely remember times for is Banjo-Tooie, which I think was about 150-160 total (1X50h file, 2X30h file, 2X20h file, + some time on the minigames)
