Dang I gotta start reading Megatokyo again, I forgot just how much I identified with that comic... gonna have to make time for it again now. I used to read a TON of webcomics (I had "the list" going too), but now i've cut down to a select few for time considerations. Mostly popular ones, and even a lot of the more obscure comics i've read have been mentioned, so i'll only drop two names...
Polymer City Chronicles (PCC) - I'm in love with this guys artwork. Even the early stuff is great. And its got a whole insanely convoluted story behind the whole thing, involving everything from aliens to the undead that I find interesting. I don't think its possible to sum things up in a neat little paragraph, you'll have to read the whole 6 year archive yourself (not all of it is story though). I guess some people might be put off by some of the *ahem* art, but I find the buff-chix and beachball sized boobs thing kinda funny. Its a slow updater (two a week if you're lucky), but its a fun little comic with plenty of story/drama/humour/mystery/sex/scifi/etc.
The other is...
Kidd Radd - Unfortunatly its over and done with, the artist had a story mapped out and finished it some two years ago. But I really enjoyed the whole thing while it lasted (600 strips). Its a sprite comic (sorta like 8-Bit), but its
animated (oooh!). Basically it involves 'Kidd Radd' (the hero) and his journey though a sort of sprite-universe with a whole bunch of other characters (including his "girlfriend", Sheena), and some narration too. It shouldn't take too long to rip through the whole thing, and I highly reccomend it. Its a great little piece of existential what-if kinda introspective, from the viewpoint of, well, a video-game character (you'll have to get a few strips in before it really "starts"... it sorta breaks the 4th wall, sorta doesn't... just check it out

). With plenty of humour, of course. Again, I really reccomend reading it if you have time.
Infact, I think im going to go re-read some of it now. *Zips off*