During her transformation, Madoka is dancing (and jumping!) with the soul gem on her head.
Hitomi having a freakout when Kyosuke reveals he turned down hanging out with her in favor of his violin practice for the nth time. Specifically where she air-juggles a pillow with a series of punches before rounding it out with an honest to god Shoryuken.
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.
It's less funny if you think about the symbolism of how Sayaka became a witch in the anime.
Even less if you remember what Kyubey does to Grief Seeds, and therefore, Soul Gems.
Same scene, blu-ray version: Mami takes her eyes off her lunch for a second, and almost instantly Bebe starts helping herself. A few seconds later, Mami has a hand on Bebe's head, holding her back from stealing the rest of her lunch.
Same scene, manga version : The food made by Homura now resembles the faces of Kyubey, Bebe and magical girls.
The scene in the flower field is heartwarming, tearjerking and les-tastic in equal measure. But when Homura has her Eureka Moment, one of the Zeppelins from Another World shines its spotlight down on the two of them, in a literal "the lightbulb goes off" moment completely out of place in such a scene. Of course, it becomes slightly less funny when you realize this was pretty much the exact moment Homucifer was born.
The intro fight against the Nightmare. Words simply do not do it justice, so here it is. Highlights include:
The Nightmare's squeaky-toy sounds and the ridiculous nature of its attacks.
The first clear shot we get of Mami? An egregious closeup of her boobs.
Madoka nearly pwning herself with her own attack.
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: she runs in circles joyfully before tripping and falling adorably on her face. And Bebe's idea of a "treat" after defeating Nightmare? "Mascarpone, mascarpone, mascarpone!"
Mami humming Credens Justitiam (her transformation song) while brushing her hair near the beginning.
At one point, Homura enters a "Tunnel of Love"-like boat ride with cartoonish paper cutouts of Kyoko, Mami and Sayaka to emphasize the fact that the fake world is making a mockery of Madoka's rules. The Sayaka one has the stupidest face. It's probably how Homura sees her.
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 facepalming: "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 Walpurgisnacht's narm-tastic green elephant.
Mami's Tiro Finale Railway Cannon is ridiculous and awesome in equal measure. Nagisa getting caught up in the shockwave and sent flying is pretty funny as well. What's TRULY hilarious is afterwards: Mami is tending to her, and Nagisa has her Bebe face on, with a dazed, googly-eyed expression.
The end sequence where Mami saves Nagisa from a cheese-a-lanche.