"Girl Genius" is what every webcomic wants to be when it grows up. The art is incredible, the story is captivating, and the blend of comedy, drama, and action is perfect. There's a reason this is at the top of the list. If you've never read it, clear a couple of days from your calendar and read it from the beginning.
Two fanboys (and one fangirl) ... Nintendo vs. Sony vs. Xbox! And cosplay!
The current project of Narbonic creator Shaenon Garrity (with Wells as co-writer). Skin Horse is a government agency, permanently understaffed and underfunded, which provides services to non-human intelligent beings. Any description doesn't do it justice; just read it.
Indie rock, hipster romance, and little robots combine to make one of the best webcomics around. Mostly a slice-of-life comic, with just enough strange elements thrown in to keep you off guard. Recommended for mature audiences (language and adult situations).
Jenny Everywhere is an open source character that anyone can adapt to their own works. She exists in all worlds, all realities, all dimensions. But then, why is she afraid of dying? And who is after her?
The following comics are no longer updating, but are still a good read.
"Narbonic" originally ran from 2000 to 2006; it's currently being re-run with the author's commentary for each strip. (Or you can read the entire original archives without commentary, starting here.) It's the story of young mad scientist Helen B. Narbon, her hapless technician Dave, Mell the violence-loving intern, Artie the superintelligent gerbil, and a host of other characters striving for world conquest.
The land of Cerealia is torn apart, as the breakfast mascots wage war for the fate of their land. The artwork in this epic story is excellent, and the amout of research that went into finding old cereal characters (from as far back as the 1950's) is amazing.
Snooty 'nuff? Funny toons.