Tales of Symphonia is among the best games on the Gamecube, both wonderfully representing and subverting JRPG tropes and conventions, with a fun combat system to boot. It also has the Ymir Forest, an obtuse, frustrating maze with an obtuse, frustrating puzzle.
While I largely like it better than many Zelda fans, the bug-hunts in Twilight Princess were terrible. The opening in the village was also boring, and felt too much like a meh-ish fantasy title instead of a Zelda game. Actually, come to think of it, the first 3rd or so of Twilight Princess felt like a poor fantasy game pretending to be a Zelda game (other than the Goron Mines, that was great).
Oh, and even though I absolutely adore MGS3, knocking out the Major and taking his clothing is pretty much impossible, unless you somehow manage to kill all the guards that aren't him or just wait for him to conveniently waltz into the un-guarded locker room for your CQCing pleasure.