One of the only games I´m sure I´ve played so much time is Sonic 3 & Knuckles. For about 2 years, I played it 2-3 hours almost every day.
Another good candidates:
-Super Mario Bros 3 (playing since 1992, beaten so many times it´s probably well over 100 hours)
-Shenmue (20-25 hours first time, and about 60 the second one, that makes close to 100)
-Final Fantasy VI (between the 3 times I´ve finished it, they probably are more than 100 hours
-Shining Force 2 (finished 5-6 times, at 15-20 hours...)