From the Season 2 finale, when Victor discovers Mara and Mick talking in the hallway:
Victor: Mick Campell, Mara Jaffray, why are you not in your rooms?! (double take) Mick Campbell?!
And afterward, the way he shouted 'BED!' loudly and slowly, as well as the scared double takes the others make, is quite amusing. And after muttering to himself that he's let things slip, he quite loudly and hammily yells his usual words.
Season 3 premire: Fabian, upon realizing that KT is American, asks if she knows Nina. KT gives us a delightful response:
Dexter: He said it! That's like his catchphrase! (About Victor's pin drop speech)
Jerome: (Deadpan) Dude, we know.
How about the camera scene from season 1?
Victor reading Amber's diary. We get this little gem...
Victor: (reading) How can a man with such perfectly groomed facial hair be so horrid?
After which he promptly stops reading and checks his mustache in the mirror.
After Eddie's rousing speech during the dodgeball game, everyone is excited except for Jerome who is wearing a look of complete annoyance, due to being pegged hard with the dodgeballs before.
Fabian gives us two little gems in the same scene-
Eddie: I kissed Patricia...
Fabian: And now you're a zombie!
The second one happens when he's leaving the room. He passes by Patricia, and, due to hearing that Alfie and Eddie were both crushing on her, he backs away from her and says, "Get away from me," while she just looks at him.
Basically anytime the characters snark each other.
Mr. Sweet as a sinner, hamming it up the entire time. Telling a random student, "YOU LOOK LIKE AN ORANGUTAN," is just one of his many over the top lines.
The sinners in general. Sure, they're evil, but they have some of the best moments, and you can tell the actors were having a blast. Alfie was probably the funniest other than Mr. Sweet, especially when he started going through Jerome's phone to text everyone about a party (in order to turn them into sinners.) It's just his blunt lines that sell it.
Alfie: It must suck to be Jerome Clarke.
Speaking of sinners, their parody of Victor's catchphrase.
Patricia: It's Ammut O'clock!
Fabian: You have five minutes precisely...
Alfie: And then I want to hear all of you drop.
Mick and Fabian slow dancing during the season 1 finale. The other characters also found it completely hysterical, and proceeded to tease them for it.
Speaking of Mick and Fabian, they had another moment in an earlier episode, this time as a Funny Background Event. While Jason was telling the class of their current exercise- partners saying "I love you" to each-other and using their tones to change the meaning behind what was being said- and Jerome is with Mara, the two are seen in the background, standing very close together, giving a quick side glance, and then moving farther apart. They then can be seen awkwardly doing said exercise.
There was also the famous "fruitbowl" incident. In one scene, Fabian was sitting at the table reaching for fruit when Mick walked in angrily and ended up taking the entire bowl away with him, leaving Fabian reaching out in vain to try and get some of the fruit before the bowl disappeared, and failing. The best part was that Mick never even noticed.