Am I the only one who didn't find the last level of Psychonauts that hard? I mean sure it was annoying but it only took me one or two tries. No, the part of Psychonauts I hated was the dance party. It's fine and dandy when you're just going through for the sake of going through, but if you're out to collect everything and get 100% by the end of the game, then good FUCKING luck spotting the figments! Thanks to the colour scheme of the whole goddamn level, a healthy amount of the figments blend right into the background, so much so that it can actually be difficult to spot a figment that's right in front of you! And then of course, there's the race in the middle, which combines figments blending in AND the fact that you're tearing through a linear course at breakneck speed. Grrr...
Jet Force Gemini is another game that I love. It's fast paced, it's music score and sound effects are all spot on, the weapons are fun to use, the controls are (mostly) easy to use. And then you get to the second half of the game, which is spent backtracking like crazy through all of the other levels with each character. Of course, on top of that there's the Tribal Collection Quest, where the guy who's been "helping" you outright tells you he has a piece for the spaceship that you're trying to repair, but he won't give it to you unless you save every single individual member of his entire race scattered across every space station, planet, and random goddamn moon.
In Batman: Arkham Asylum, Batman's knees are really thin and disproportionate compared to the rest of his legs. Yeah it's nit picky, but it looks really weird and I just can't get over it.
Tiny Huge Island in Super Mario 64 annoys the hell out of me. There's a lot of awkward jumps and the camera just seems to be wholly intent on getting you killed in that level.
Saints Row 2 is a total blast (especially with a friend), but the Snatch and Escort minigames are horrible to fight through. What makes it worse is that the Snatch minigame offer two of the best rewards depending on which version you do (2/3x faster health regen or GAL 43's and unlimited SMG ammo). You can totally ignore Escort (the worst minigame in the game by far for the sheer amount of nonsense it throws at you, and the rewards aren't even worth it), but the fact that it's even there is enough to annoy me now.
Oolite is loads of fun and I have a blast almost every time I play. However, Oolite also has a tendency to just say "fuck you" at points and I end up in situations where I survive solely on luck rather than my ability to fly/fight.