gmpalmer wrote:Sluggy Freelance -- One of the longest running webcomix and of those that old (with a continual story line) my favorite. Warning, may branch off into seemingly tangential storylines for 6 months or more.
First webcomic I ever read, starting way back in 2001, and it's still just incredibly nifty.
A few other good ones that haven't been mentioned:
http://www.drunkduck.com/The_Dragon_Doctors/index.php?p=619573 The Dragon Doctors. Recently started, really good; fantasy storyline. Note that the artist has an interesting habit of first posting a pencil sketch of his most recent strip, then posting a full version later, so if the most recent one looks rough that's why.
http://egscomics.com/ El Goonish Shive. Been running a long time. Dosn't update that regularly, and storylines take a long time to go anywhere, but it's always interesting.
http://galactanet.com/comic/ Casey and Andy. This webcomic is finished now, the story is done and it is no longer updating, but if you haven't read the archives, you need to; it's just incredibly funny. "Two mad scientists who periodically die".