I read quite a few on a regular basis, but my top three are:
Girl Genius is my third most favorite. It's a bit difficult to get into at first, since it just throws you into a situation where you aren't connected to the characters, so it seems uninteresting for a little while. However, if you become interested, and work past that point, you will find quirky humor, a creative world, and many deeply fleshed out (if OP
) characters.
Goblins is my second favorite. It started as a semi-generic slapstick D&D webcomic, but quickly turned into an incredible storyline. The colors are vibrant, the characters become real, and the writing is amazing. The only reason I don't place this above and beyond anything else I've touched is that there are only two updates a week, and the author occasionally misses updates due to various reasons even then. Despite this, it's brilliant webcomic.
My favorite webcomic is called Schlock Mercenary. Space mercenaries who deliver a laugh every day. The story sometimes moves slowly, due to spending time on humor, and the fact that each daily update (aside from Sunday, which is much longer) is only one line of panels, but the writer keeps you entertained, and still manages to move at a steady pace. The artwork as improved over the years, and is quite good, and these characters are also well written and likeable. There are enough that they cannot be fleshed out as much as those in Goblins, but there are still a core of characters whose personalities are quite distinct. While I cannot press any particular point forward as the webcomic's quality that makes it so good, the overall combination leaves nothing (at least for me) to be desired, and it truly is a great webcomic.