Most of my favourite webcomics have already been mentioned, I'll just repeat the best ones.
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Adventures of Dr McNinja is probably my overall favourite, it's just fantastic ("What would Batman do?"
). Every time you think it has jumped the shark, it one-ups itself. One of the rare webcomics that manages to get me into can't-stop-laughing-please-it-hurts mode. Anyone else read this, aside from Titandrake?
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Order of the Stick, for the story and characters, even though it doesn't take itself seriously at first and I've never played D&D. It still manages to be funny after growing a thickened plot, which is quite impressive.
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Gunnerkrigg Court, it's just so intriguing (the art gets better, indeed). Alternates zanny humour, mysterious magic, and some light nightmare fuel.
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8-bit theater is crushingly funny if you are into nonsensical plots, callbacks, and dark humour.
Also, I wish
Perry Bible Fellowship kept updating
Haven't been mentioned yet:-
Derelict, a post apocalyptic story of a girl and her boat, simply trying to survive. A strange fog has turned people into Gargoyles, the plot evolves around the origin of that. It's cool!
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Next Town Over. The art is ****ing amazing,
miles ahead of everything else I've seen. Setting: western. A zombified bounty hunter seeks to kill a necro-pyromancer, and it's not clear who you should root for. The archive is not very long yet, go read it RIGHT NAOH!
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The Abominable Charles Christopher. The only webcomic that isn't miles behind of Next Town Over in the art department. It's amazing how much emotion the author can work into animals without actually antropomorphizing (is that a word?) them. You'll cry because it's beautiful, you'll cry because it's sad. The story is an intriguing remix of the Epic of Gilgamesh. Need I say more?
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Powernap. Updates very infrequently though. A futuristic society where a drug obsoletes sleep... unless you are allergic to it. Onyric sequences mix with corporation intrigue. Nice art too!
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Dresden Codak. Updates like once every lunar eclipse. Interesting story about the Singularity, and other not-quite-yet-relevant-buy-maybe-shortly-in-the-future philosophical and ethical questions. The first chapter looks like it was made under the influence of some potent shrooms, it becomes sliiiiightly easier to follow afterwards. The art is nice, and the story very much not traditional.
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Chimneyspeak, a story about murder and prostitution and revenge and a midget in (Victorian?) London, very NSFW. I don't know if you can find it online anymore, though...
If you don't much care for story:-
Manly guys doing manly things, jokes about VG characters and comics and stuff. The author keeps a regular weekly schedule, yet can't always dedicate enough time to it. The good jokes are very funny, but sadly there's a lot of filler.
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Foxtrot, by Bill Amend. It's Foxtrot.
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Two guys and Guy. Self-deprecating humour about a hateful girl, a mad scientist with no social skills, and a good-for-nothing dude.
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Gone with the blastwave. Apocalyptic (very) dark humour. Short, updates close to never. Funny.
Probably forgetting stuff, and I am keeping some that I follow but aren't that good for myself, this post is long enough as is.