Oh my a thread about webcomics? Let me open my favourites bar and jus- woah ho, how did I read this many? Ok, we'll go with my favourites
1) Homestuck. If you stick with it you'll discover what is, in my opinion, the greatest work of fiction placed upon this earth, and I've read hundreds of books and dozens of webcomics.
2) Dresden Codak. Gorgeous art. Gorgeous nerdisms. Gorgeous creator. The most science filled webcomic I've ever read, and it's update schedule is like once a month but worth the wait.
3)Achewood. Alcoholic cats. Retarded stuffed otters. The Great Outdoor Fight. Mexican cameras that show how what you think of yourself. Named after a slave brew that caused depression and brain damage. Genius.
4) A Lesson is Learned but the Damage is Irreversible. Forget everything you learned about comics, plotting, continuity and logic. Make everything look like Braid. ?????? Profit!
5) Nedroid. The friendliest comic ever made, a bird called Reginald and his best friend Beartato have fun adventures, occasionally with Harrison the shark and Gary the robot, it's the nicest thing you'll read all day.