Of course, now that this has been revived I do need to add a few other great non-mainstream comics:
Kate Beaton's "Hark! A Vagrant" (Yay for historical humor! Over recent times it does seem to have increased in popularity, so I'm sure at least some of you have heard of it.):
http://www.harkavagrant.com/Ryan Armand's "Great" (By the same guy that did Minus. One of the few comics I've been reading since the start, and now that it's been linked to by Ryan North of Dinosaur comics, I imagine it'll get a bit more notice):
http://www.kiwisbybeat.com/great1.htmlJustin Pierce's "Wonderella" (Like Wonder Woman but clearly not. Great parody. Hilarious comic):
http://nonadventures.com/2006/09/09/the-torment-of-a-thousand-yesterdays/ Peter and Erin Donahue's "Pear-Pear": (Personally, I never thought I could find a wordless Pear and Mug such compelling characters. It's strange, but a huge amount of fun if you can get into it. Surprised this isn't more widely read):
http://www.pear-pear.com/archive1.htmSeriously, read all of those. They are fantastic.