I don't know that I have an absolute favorite so I'll plug the ones nobody ever talks about.
GPF Comics: Very awesome story, and releases every day in
color.
Todd and Penguin: TAP for short, Penguin is uber cute and I
happen to have a thing about penguins so....
RWWR (Reasons Why We Rule): Hilarious comic, just hilarious.
Others:
I read MT, used to love it but I'm not really enjoying it as much anymore. It's become too drawn out and
Fred's little year or cons made it seem too commercial/sold out. Still love it and Fred but I just can't say
it's my absolute favorite.
Real Life Comics is way too true to my/my friends life. Esp. the whole piloting eva, travelling to the past, etc parts.
You'd be surprised just how habitable Mars is. Can't beat the humor in that comic.
LOVE Chugworth, Applegeeks, and PA too... That's a list of my favs, yup.