I've read a lot of webcomics over the years, and I can't really remember them all.
I read Order of the Stick and Erfworld, and thank God for them. They're awesome. Awkward Zombie is awesome, too. Go Katie go!
I also read Dueling Analogs, Phil and Dixie and VG Cats, but the former two aren't really that funny and the author has pretty much given up on the second one.
There are some others I read that aren't active anymore. This Comic Sucks ended a while ago, but I really enjoyed it. I don't know if the archives are still around. F@nboy$ was good while it lasted, but Krudman finally admitted he had stopped caring about the comic long after everyone already figured it out anyway. The venerable 8-Bit Theater has come to a close, though it does have a final epilogue comic coming shortly, and his new comic(s) are marginally entertaining. Shamus Young's two finished comics, Chainmail Bikini and DM of the Rings, are really, really funny and super mega hyper extraordinarily funny, respectively. I've also really enjoyed the Krakow comics, but I stopped reading them for a while; to me, the original Krakow and Krakow 2.0 are still more entertaining than the more recent works: Marilith fell completely flat to me, and Charliehorse is solid but uninspired. His latest work, Spinerette, seems very, very promising so far, though.
Although I never actually read it while it was running, The Last Days of Foxhound not only manages the (extremely easy) tasks of being far, far more entertaining and intelligent than anything Hideo Kojima has ever written, but goes the extra mile and makes the canon events of the Metal Gear Solid series actually make sense, a feat so unlikely that Chris Doucette should be worshiped as a god.
There are a few comics I have... 'mixed' feelings about. I read Questionable Content and CTRL+ALT+DEL early and often for a long time, but eventually dropped them, both on account of how the authors started to more and more often hijack their own works to spout insane, ham-handed social, moral or political commentary. More importantly, both of them also offered me a moment where I suddenly sat bolt upright and thought, "Wait- he wants me to take these characters seriously?!" In both cases, this revelation quickly precipitated my undying pity for both of these works.
Penny Arcade is an interesting case. It's absolutely legendary, and I finally sat down not long ago and read through the entire archive. What I noticed is that there is a fault line right at the beginning of 2006. Everything before it is uniformly terrible and physically painful to read, and everything after that has a 2/3rds chance of being exactly that bad and a 1/3rd chance of being tremendously hilarious. However, as has been said before, the two guys behind the comic have done so much for charity that, and I'm quoting as best I can here, "they could both eat a live baby and still be considered pretty good guys." That's definitely true, and as such I have to take off my hat to them.