In Wind Waker, the Triforce Hunt, and also the Savage Labyrinth. Both suck, but the rest of the game is gold and the final encounter is amazing.
In Megaman X8, Gigavolt Man 'o War’s stage. The rest of the game ranges from good to great. Seriously, do Gigavolt’s stage first; there are no secrets and once it’s done you never, ever have to go back.
In Final Fantasy 6, the large gaps in the game’s second half that are devoid of the same great narrative found in the game’s first half.
In Final Fantasy Tactics, getting into a random battle with 5 Calculators who all know Life/Raise spells. Seriously, just reset. The 10+ Monk random encounter is almost as bad.
In Gears of War, the vehicle segment.
In Gears of War 2, the entire first vehicle segment and portions of the second (the second also has great, Panzer Dragoon-esque sections). The third vehicle segment is pretty damn fun.
In Halo, the Library and any Flood-heavy section.
In Halo 3, that third-last level everybody hates with good reason.
Building spell levels in Secret of Mana. Levelling in general, actually, but that’s another rant.
Some of the mini-games in Mario and Luigi 3, otherwise one of the DS’s best titles.
Illusion of Gaia. Ankhor Wat (sp?). Kill me now.
Any Sonic zone with the word “Marble” in its name.
Most of Symphony of the Night, a rather overrated game, including the various unpopulated long hallways in the first castle and most of the second castle.
Dr. B has no boring or hate in his being. Only love. Sexy man-love, for all willing to love back. No homo.