Lets see...
I'll third Gunnerkrigg Court, and second El Goonish Shive.
Other ones I follow that I don't think have been mentioned yet are:
Fatherhood - A weekly webcomic my brother started writing when his wife was pregnant with their first child (I think it's funny, and as he's family, I feel required to plug it.
)
Two Lumps: The Adventures of Eben and Snooch - a pair of cats. Includes jokes about the weather in Texas (where the author lives), silly stuff cats do, etc
Goblins - following a group of D&D style goblins (lots of gamer humor mixed in)
Looking For Group - a fantasy adventure/comedy loosely based on/inspired by World of Warcraft I believe, though it's diverged a fair bit over the years.
Schlock Mercenary - long running daily comic about a scifi mercenary force. Like with so many long running webcomics, the art has improved over the years.
Naruto: Jutsu and Jinchuriki - I haven't read too far in this one yet, but in the tradition of Darths and Droids, or Friendship is Dragons, it's a Naruto as tabletop campaign webcomic.
I'll third Gunnerkrigg Court, and second El Goonish Shive.
Other ones I follow that I don't think have been mentioned yet are:
Fatherhood - A weekly webcomic my brother started writing when his wife was pregnant with their first child (I think it's funny, and as he's family, I feel required to plug it.
)Two Lumps: The Adventures of Eben and Snooch - a pair of cats. Includes jokes about the weather in Texas (where the author lives), silly stuff cats do, etc
Goblins - following a group of D&D style goblins (lots of gamer humor mixed in)
Looking For Group - a fantasy adventure/comedy loosely based on/inspired by World of Warcraft I believe, though it's diverged a fair bit over the years.
Schlock Mercenary - long running daily comic about a scifi mercenary force. Like with so many long running webcomics, the art has improved over the years.
Naruto: Jutsu and Jinchuriki - I haven't read too far in this one yet, but in the tradition of Darths and Droids, or Friendship is Dragons, it's a Naruto as tabletop campaign webcomic.