Silent Hill 2 - Voice acting and writing was...uneven. Very high points (Angela on the staircase), very low points (Angela in the graveyard) "...LOST?"
Baldur's Gate 2 - Um. I...I can't do it. I really can't think of anything. I'd pick at Throne of Bhaal for being an incomplete sequel, but the Ascension mod fixes that up a fair bit and makes the final fight absolutely amazingly epic in every sense of the word.
Mass Effect 2 - Didn't get enough time to talk to Legion without letting my crew turn into Jello. Also, I missed the random planet exploring, although the Hammerhead DLC fixes that a little. And give me back my skill trees, dammit.
Team Fortress 2 - This is really stretching it, but with all the new content and weapons, anyone just picking the game up now would probably be completely lost in a sea of too many choices. Then again, why the hell are you just picking it up now?
Half-Life 2 - Route Canal drags a little bit. Not enough Barney time, and...uhh...they never told me what happened to that cat?
Psychonauts - Boss battles could've used some more strategery? You had all those different cool abilities, and hardly ever needed to use them. Final boss was just kinda "run away, get big, punch boss, get small, run away," rinse & repeat until done.
Planescape: Torment - Difficult to find out where to go except through talking to absolutely everyone. UI is a bit clunky.
Tachyon: The Fringe - Needs a joystick in order to fully appreciate. I don't have one anymore, and I have a laptop. ;_;