Perry Bible Fellowship is excellent, excellent stuff. I only wish Gurewitch would begin updating it again.
Cave Explorer, Sgt. Grumbles and Dinosaur Meteors are probably my favorites.
Edit: BUT NONE SO MUCH AS COMMANDER CRISP OH GOD HOW DID I FORGET
i agree, the pbf comics are probably my favorite web comics. the only one i really follow right now is xkcd, but he does a lot of math jokes. like, i didnt even know you could make that many math jokes.