(Warning: Not safe for Liberal Majors)http://www.irregularwebcomic.net/
Unspeaking Vault of Doooooooom:http://www.goominet.com/unspeakable-vault/
Darth and Droidshttp://www.darthsanddroids.net/
Cyanide and Happinesshttp://www.explosm.net/comics/
Rusty and Co.
Defunct due to copyright issue with Wizard of the Coast.
Flintlocke's Guide to Azeroth (ended)http://pc.gamespy.com/articles/578/578734p1.html
Few other that was already mention:
Dr.Mcninja, Questionable Content, Pictures for Sad Children, Saturday Morning Breakfast Cereal, 8-Bit (ended), Perry Bible Fellowship, Order of the Stick, Gunnerkrigg Court, VG Cats, Super Effective, Dilbert, Pvponline (and soon Table Titans), Penny Arcade,
Comics to Run away from very fast:
Real Life comics (Got really lame after a long run due to writer running out of ideas)
LFG Comics (blagant rip off on 8-bit, with WoW reference and narcissism thrown in)
Least I could do (Writer Ego Stroke)
Megatokyo (Started off amazing... then the writer and the artist have "creative differences" and the writer left... the artwork really hasn't evolved, the storyline tanked)
Ctrl-Alt-Del: Tim Buckley is a complete dick.