Dungeon Keeper, Startopia and Gothic 1 & 2, Serious Sam TFE and TSE have some good fun moments, details and goofy secrets.

343 Halo games.
But not intentionally funny.

Superheroe league of hoboken.

Xcom 94' was funny when I started shooting my own soldiers when they run into chryssalids.

Fallout 2 had some good laughs.

The GTA games were funny up to 5 then I can't even remember anything funny about them other than one of the guys was far too much like somebody I know.

I enjoyed the south park games

Pain.

It was a PS3 game (I think exclusive) where you shoot yourself out of a giant slingshot to see how much damage you can do to yourself/the city.

A lot of the static gags are immature humor that's not really my thing, like farts and sex jokes and such, but what really makes it funny is the crazy physics. Your dude is pure ragdoll, which at the time was still in its infancy, so it's kind of hilarious. Then a lot of the stuff in the game explodes for no (obvious?) reason, and you can actually grab onto stuff, which can be amusing when it's a car, or a flagpole, or the giant bowling ball on top of the bowling alley, or whatever.

Now I kinda wanna go play that game some more, lol.

Worms