This line from Junko: "Us adults are always in pain. That's why we can drink alcohol!"
Homura saying to Madoka in front of the whole class that she is now a Magical Girl like her. Madoka's face here is priceless.
Followed by Homura practicing her Time Stop powers for the first time by using them to rather clumsily beat up a garbage can in midair with a golf club which is rather amusing considering we've spent nine episodes seeing her as a Stoic Bad Ass.
Madoka getting low scores on her English test and she's worried about it. Sayaka, on the other hand flunked most of her tests, and acts like its not a big deal.
In a case of Hypocritical Humor, Sayaka thought Homura used her time stop powers to get high scores on exams, and suggests that she use it to get the answer sheet for the make up test. Apparently she's the only one to have this (brilliant) idea. Near the end of the story Homura offers to use her powers so Madoka can pass her exam.
Homura flat-out telling Madoka that she should be spending her time studying instead of brainstorming cool names for her special attacks, since all her ideas are lame.
Mami's theme continuing to play even if the target that she is aiming at is actually a cat.
The final scene with Madoka and Kyubey in the bath.
One darklyhilarious moment in this track at 16:34 is from a doujin that, while depicting Sayaka saying "I'm such an idiot-", shows the her expression when saying the line in the show immediately before transforming into a witch.
One that stands out is Homura in Shrinking Violet mode telling Madoka "I think you have a great ass..."; you could imagine her thinking it, but she, as she is at the moment, perhaps the last character you would expect to say it out loud.
Christine Cabanos demonstrates her sense of comic timing in this outtake:
Kyubey: So, if you ever feel like dying for the sake of the universe, call me. I'll be waiting. (fades away)
In an interview with Urobuchi and Shinbo on the English-language volume 2, they suggest they'd like to do a spinoff about Madoka's mother learning the art of manipulation from Kyubey and using it to hijack her company.
In the first Drama CD, Sayaka gives Madoka and Shrinking Violet Homura some well-written math notes to help them out... only to immediately reveal that she stole them from Hitomi.