Anders Loves Maria – by Rene Engström – The travails of love in Sweden. Starts out sweet, and then the characters turn into self-involved assholes. I'm still reading it, though.
Angels 2200 – by Peter Haynes, Nathaniel Savio, Jana Hoffmann, Kimberly Stewart – Though it's on quite a bit of hiarus right now the updates still come in, it is a good story so far.
Digital Pimp Online – by Joe Dunn – Home of Joe Loves Crappy Movies, Free Lunch, Retail Rage, Matriculated, Fish Tank Tango, Turtle Vs. Bunny: Distractions, and Another Videogame Webcomic, all by the comic powerhouse Joe Dunn
Goblins – by Tarol Hunt, Danielle Stephens – D&D reconstruction through the eyes of a group of goblins who got tired of being XP fodder and started their own adventuring party. Gory.
Narbonic – by Shaenon K. Garrity – The ultimate mad-scientist webcomic. This finished a few years ago, and is now in Director's Cut reruns, but its six-year run is one of the best examples of a consistently funny, engaging story in webcomics, and also a good example of a comic that ended when the story was done, rather than stretching itself out unnecessarily. The early art's a little crude, but it grows on you and gets better. You should definitely give this a look.
Nedroid Picture Diary – by Anthony Clark – A hilarious comic by the colorist of Dr. McNinja.
Nerf NOW!! – by Josué Pereira – Primarily TF2 based webcomic.
Octopus Pie – by Meredith Gran – Great-looking, funny, and consistently surprising, with a writing style that prizes detail over narrative. You might have to go through a story twice to see exactly how all the individual comics fit together, but you'll also find a wealth of character detail on that second go-through, so it's really worth it.
Scary Go Round – by John Allison – It takes awhile to get used to the humor, and the archives are too bloated to recommend going through, but this is still a fun strip.
Sister Claire – by Yamino – It's new, so far it has been interesting.
Skin Horse – by Shaenon Garrity – Similar to her previous strip (Narbonic), but with much better art, and even more bizarre characters, including a transvestite black-ops agent, a violence-loving zombie, and a talking dog who is better at surpressing her animal instinct than either of her co-workers.
Slow Wave – by Jesse Reklaw, people's dreaming minds
Starslip Crisis – by Kris Straub – Great sci-fi strip, and one of the first strips I've seen in a long time that consistently does original things with time travel. Straub's other strips, chainsawsuit, F-Chords, are also worth a look- I can't wait until F-Chords comes back.
Subnormality – by Winston Rowntree – Sphinxie!!!! Squeeeeeeeeeeeee!!!!!
The Meek – by Der-shing Helmer – Man, I ate that one right up. So good. Also, as a head's up, it's a little NSFW as the main girl is running around topless at the moment.
the outer circle – by Steve Napierski – Same author as Dueling Analogs. Updates infrequently of late, but the archives are vast, full of humor perfect for the preadolescent male, which is right where I try to keep mine.