http://www.samandfuzzy.com/ basically there was a strip where the main character has a run in with the Ninja Mafia, and then it became the whole plot. Good stuff. Right now is guest strip week.
http://www.darthsanddroids.net/ Star Wars doesn't exist but a D&D campaign "just happens" to follow the plot. "Ok so I buy these sweet monk robes" "dude, you should get laser armor" "no way. Now I need to buy a laser gun, oh crap I don't have any money. Now I have to buy a crappy laser sword. Damn it." ------ "Hey guys I have to babysit my sister so she is going to hang around" "Sure, now you guys are on Naboo and you want to talk to the Governor of the province" "Sister: No, No, No you decide to go talk to the princess. Who is 12 years old, and the people love her so much that they elected her as princess, forever" "what??!?!" "and she is on the other side of the planet" ------ also Jar Jar Binks is cool in this version
http://cdc.comicgenesis.com/: rare, not well known webcomic that is really funny.
http://www.giantitp.com/comics/oots0001.html: stick figures in a D&D setting
http://antihero.keenspot.com/ : a funny batman like guy with a gun. OK not really, but still good.
WTF comics (thats what it is called)
http://www.sluggy.com/: One of the longest running and most popular webcomics of all time. Currently going on a very very epic run of events. Also really funny
"so I was in hell and I spilled coffee on my sweater and..." "why would you be wearing a sweater and drinking coffee" "listen lady, what do you think we do there huh. Drink margaritas and wear shorts on the beach and dancing to Duran Duran. NO. We drink coffee and wear sweaters. Why? BECAUSE WE ARE IN HELL".