My personal favorites as of right now:
1. The Life of Riley at clanbob.net.
2. 8-bit Theater (check out the flash version here at Newgrounds.com).
3. Sparkling Generation Valkyrie Yuuki (wish the author would update more often)
4. Sara and David (first 3D anime webcomic I've seen, there are I think two flash comic here).
5. Sakiria (author is pondering the storyline a lot, so updates are sparce).
6. Sore Thumbs (pretty cool)
7. Dominic Deegan (updates almost every day!)
8. Slackers (cool web comic)
9. Crimson Moon (maybe the most beautifully drawn web comic ever)
10. Krakow (kinda stupid and humorous, just throwing it here for kicks.)
Those are my personal top ten.