(The numbers indicate the number of updates per week.)
6 Narbonic — a very funny (IMO) gag-a-day strip with sustained storylines (nearly every strip has both a gag and advances the plot). It's a mad-scientist setting, so the plots may sort of seem like the obvious random mad science things — cloning, gender swapping, time travel, transmogrification, and secret moon bases; but the characters stay true to their weird and mostly-evil leanings, and underneath the seemingly mad scientist trope plots lie a surprisingly sophisticated arc has been slowly building. Narbonic is part of Modern Tales, which requires a subscription to read the archives; however, until July 3rd you can read the archives for free. Then you just have to make sure you don't miss a day after that. The first two times I tried to read Narbonic it was a total lose; it wasn't until I read all the way through the archives that I was sold.
3 Girl Genius — another mad science comic, this one by Phil Foglio of Buck Godot, XXXenophiles, Dragon Magazine's "What's New", and a few Magic: The Gathering cards. Foglio has a very distinctive cartooned-character style (his MtG cards looked totally out of place to me), but I think it serves the humor fine. But while most people are familiar with his humor, I think he actually excels at world building or at least backstory; Buck Godot has a very interesting setting involving the "law machines", although wikipedia fails to give any detail so I'm not bothering to link. Girl Genius has so far engaged in some nice "the villain isn't really a villain—or is he" business , leaving things much more grey-shaded than expected. Also, mad scientists in the Girl Genuis universe have some charismatic power that causes people to be overly-obedient to them, and it's not clear how much that's involved in some of the things that have occurred in the series so far.
2 Miracle of Science — currently on hiatus for another two weeks, and I posted about it recently, but I'll list it here since it's the other mad science comic I read. It's a sort of manga-inspired art style with a semi-hard-science setting — but the story isn't really about science, it's about mad science, here determined to be a disease that causes the mad scientists to act exactly like cliched Hollywood mad scientists. Which is an... interesting... direction to go. There have been a couple decent twists along the way, but I do worry, on re-reading, that some fairly obvious things are being set up. Hopefully I'll get surprised anyway.
3 Order of the Stick — Stick-figure characters in a D&D world relentlessly mix humor and story/character stuff. The central premise is that the characters have all the knowledge the players would: they know about the rules and die rolls and all that stuff. It turns out that this can be milked for an enormous number of actually-funny-gags, even for people like me who don't even know what "feats" are in these crazy newfangled games that are also called D&D for some reason. Start at the beginning, assuming RPG humor is at all plausibly appealing.
5 Scary Go Round — British folk talk like crazy people while having incredibly goofy experiences that sometimes qualify as adventures. The plots have gotten erratic in the last six months, but really it's all about the language (although I personally love the art style, too). "God love weasels, but do they really need an aqueduct?"
5 Questionable Content — Two-to-four indier-than-you kids talk about indie bands I've never heard of and act sexy and make scarygoround-lite wacky talk. The heart of the comic is a will-they-or-won't-they romantic relationship.
1 Perry Bible Fellowship, which I've linked to before. The author has the best sense of humor ever, if you like twists. Usually three or four panels, and about 1/3rd of the time the last panel just blows me away.
And then there's:
6 Sluggy Freelance
3 Penny Arcade