Basically every single scene between Todd and Atticus.
Some members of the "gang" get up and run out of class, prompting this response from the teacher:
"Alright class, none of the other teachers will listen to me, but when those two get up and run out of a room then something bad is about to happen. If you'll excuse me I'm going to go barracade myself inside the teachers lounge till this over. I'll see ... some of you tomorrow."
In Invasion of the Stupid Snatchers, we have this line:
"And I wanna park in the handicap zone, but we don't always get what we want"
From Jungle Fever: Jenny laughing like a complete goofball at her own lame joke about a coincidence being a "Gina-incidence."
Atticus' entire interaction with Troy. It's only a few minutes long and yet manages to cram massive amounts of Homoerotic Subtext into it. To make things even more hilarious, Troy dies in the very next scene and Atticus proceed to mourn Troy for the rest of the episode, despite literally knowing him for a couple of minutes.
"I love pizza so much I don't know whether to eat it or suck it off!"
Metal dude, metal dude, metal dude wop!
Any time anyone (generally Atticus) runs out of a room screaming "Nobody understands me!"
From the Season 2 premier, after it's become apparent that the Metal Dudes are evil.
From the closing song in the second Phantom of Crowley High episode, 2 Girls, 1 Tongue, after the gang all sing about how sincerely sorry they are about some of their previous behaviour, we cut to Atticus and the Minions in the Retirement Home, who sing their own verse:
Atticus: I'm so sorry for being crazy and mad/I promise you I'll be a better leader and man.
Minions: We're so sorry but it's come to this/We must kill him after we drink.
The Minions all fall dead from the poisoned beverages Atticus gave them, while Atticus dances in the foreground, followed by: