Pretty much all of Psychonauts had me rolling with laughter. Mikhail had a few funny ones, Sasha had a bunch, and Boyd was great, but all in all, it's the "not Federal agents" that had the most amazing lines. Particularly housewife!agent. "Even though my husband is no longer sexually attracted to me, he will always love my pies."
Also, in long-forgotten No One Lives Forever 2, there are dozens and dozens of hilarious lines. But the best scene is in the level in India. The police think Cate (female James Bond) and Armstrong (angry Scottish stereotype) have murdered a guy. At the beginning of the level, you're supposed to wait for the police to go away because you can't kill them (they're civilians; killing them causes instant mission failure). This conversation follows:
Cop 1: So what did the murderers look like?
Cop 2: Well, there was a huge man with red hair and a beard wearing a skirt.
Cop 1: You mean a kilt?
Cop 2: I don't know much about women's fashion. Anyway-
I don't know why it made me laugh so hard. In retrospect, it's not that funny. But there was something about it at the time...