Funny: Puella Magi Madoka Magica The Movie Rebellion
The Cake Song. It comes out of nowhere, the background music has absolutely no coherent melody, and the whole song is sung-spoken to a weird rhythm similar to the Anthonies' equally weird chanting in Episode 1. Let alone that it's the last thing you'd expect from a Madoka movie.
Bebe is visibly excited at the prospect of "becoming cheese". Mami (as a joke) just told her that if Bebe keeps eating that much cheese, she'll turn into it herself. And Bebe's idea of a "treat" after defeating Nightmare? "Mascarpone, mascarpone, mascarpone!"
There is a perfectly climatic Kyoko/Sayaka moment in the middle of the final fight. They talk about dreams, regrets and such stuff...and then Nagisa flies past them screaming "And i just wanted to eat cheese again!". Cue to Sayaka facepalm : "Hey, we are having a moment here!"
Bebe/Charlotte/Nagisa in general, really. She's easily the most overtly childish and comical of the group.
The Climax; Madokami descending from above, majestic and glorious with appropriate background music. Following not far away behind, Sayaka and Nagisa are riding a chariot pulled by the narm-tastic Walpurgis' green elephant.
Evil!Homura getting beaned with a tomato.
"I don't get it". Said by countless Incubators just as Homura and Madoka destroy their barrier and kill them in the process.
Kyubey revealing his plan is him at his smuggest, dog-kickingest, blood-boilingest WORST. He punctuates a moment of his monologue to scratch behind his ear and under his chin like a small animal.