Okay, list time. Here it is, in a rough order of descending quality:
Schlock Mercenary - Comic about a Sci-Fi Mercenary company. Great ongoing story.
Girl Genius - Steampunk Mad Science Awesomeness!
Penny Arcade - Arguably
the video gaming comic.
The Adventures of Dr. McNinja - He's a Doctor who is also a Ninja. Need I say more?
Questionable Content - Kind of soap-opera-ish. I don't know why this comic is so interesting. It just is.
xkcd - Math Jokes + Stick Figures = Awesome
Saturday Morning Breakfast Cereal - Hilarious
Sluggy Freelance - The life of a humble web designer looks more exciting when you add mad science, aliens, alternate dimensions, shadowy conspiracies, vampires, and everything else you can imagine.
Narbonic - One of my favourite comics of all time. Mad science! Unlike most webcomics, it has a definite story with a 6 year arc. Brilliant stuff.
Skin Horse - From the mind that brought you Narbonic
Dresden Codak - hard to follow the continuity sometimes, but it's humour is pretty science-y, and it's art is pretty pretty.
Order of the Stick - Tabletop RPG humour
A Girl and her Fed - Great story-based comic
Shortpacked - Last time I checked, this was still nominally about a bunch of misfits who work at a toy shop, but now, who knows?
Antihero For Hire - Follows the adventures of an antihero named Shadehawk through a cyberpunk futuristic setting. Good stuff.
A Miracle of Science Mad Science! In The Future! This was one of my favourite comics for a while. Sadly, it ended after a 5 year run.
Ctrl-Alt-Del - Video Gaming Webcomic
Full Frontal Nerdity - Tabletop RPG Nerd Jokes. Brilliant. Made by the same guys who do
Nodwick
Goblins - What happens when the NPCs decide to become adventurers.
Bad Machinery - This has been going a while, previously as Scary-Go-Round, and I believe even before that under another name, but some characters keep getting held over into the new comics, and they do seem to maintain continuity.
Overcompensating - by the same guy who made
Wigu, but I prefer his autobiographical stuff, it's funnier.
Erfworld - lots of tabletop and board gaming references and jokes.
Real Life - Wow, is Greg Dean still going? Okay, I guess.
Bigger Than Cheeses - I quite liked this one, was sorry to see it end. Still, the archives are worth a browse. Very random, and very funny.
Hijinks Ensue - Nerds, Jokes, etc.
Dreamless - So. Pretty. Great story too.
Radioactive Panda! - More Science, possibly of the Mad Variety.
El Goonish Shrive - This comic goes to some odd places. Still, readable.
Home On The Strange - Comic about a group of nerdy friends.
8-Bit Theater - I think this one has finished up. Worth a read for the RPG jokes and references.
Looking For Group - Another RPG Comic
The Zombie Hunters - Nice little story comic about fighting zombies in a post-apocalyptic wasteland.
VG Cats - Yet another video gaming comic.
PVP - Ditto
... and that's probably a good place to stop.
Darn it, now you guys made me remember I have a backlist of things I haven't read yet either.