The entire Armadeaddon storyline counts. Hell, Jim, a completely anciliary character who was introduced as a dessicated skeleton, turns out to be the leader of the zombie horde; and one of the zombies was Gabe and Tycho's former undead roommate.
Don't forget how Tycho beats Jim: with an absolutely legendary callback joke. Specifically, the "I roll twenties", from the sandwich comic.
When Jack Thompson reneged on his offer to donate ten thousand dollars to charity if someone made the ultimate violent video game in which players could urinate on people's brains and murder kids who worked in video game stores, Mike and Jerry made the donation themselves.
Tycho: We've just made the donation you never would, and never meant to. Ten thousand dollars' worth. And we made it in your name.
The last word on bullies? "I will personally burn everything I've made to the fucking ground if I think I can catch them in the flames. -Gabe Out"
The same guy later continued to harass Mike and Penny Arcade via Twitter. He claimed to be visiting PAX in disguise even though he was banned. However, he forgot that his iPhone also tweets his location. It doesn't even stop there; read it for yourself.
One for Mike (Gabe), after going to his son's school and hearing that one of the girls loves Slenderman, he's planning to do something about the problem of kids playing violent games meant for teens or adults in a mature and reasonable manner by explaining to parents about the ESRB rating and what really happens online.
Robert Khoo is a walking CMOA. In 2002, he met Mike (Gabe) and Jerry (Tycho) and showed them a business plan he came up with for Penny Arcade and offered to do two months of work for free to try and make their webcomic a successful business, since he felt that they should be millionaires. Eleven years later, Penny Arcade is one of the most successful webcomics ever made and he manages to run it and has a huge hand in Child's Play and all of the PAX conventions.