Grandia II
I really liked the game until the dungeons started to become too large and boring. Also it was too long, a problem many JRPGs have.
Zelda: Ocarina of Time
Every few years I start replaying it, but usually stop somewhere at the later dungeons. At first the game comes with some story, but then it feels like nothing but work.
I disagree with Far Cry 1. Only the last two levels are bad, as they become extremely hard and unfair. My favourite level of the game is "Boat" or how it's called, Where you have to do island hopping. That's relatively late in the game.