Donald Duck noticing the mundane ducks in his sequence. Actually, pretty much that whole sequence when it's not busy being a tearjerker.
The multitude of rabbits getting off at the end of the voyage. Parents will get it; kids won't.
Same concept applies to "Rhapsody In Blue", though sometimes the tearjerking element and the funny overlap very nicely.
In Rhapsody in Blue, special mention goes to the scene in the Subway where you can see everyone uncomfortably packed together, (This is actually Truth in Television given how crowded that stuff can be!) If you look at the squeezed in figures, you can see a foot poking out of the crowd, and A man's armpit in a woman's face. However, the crowning moment really comes when they get off the Subway, are still crowded, and are holding invisible handguards. They even walk like this, too!
Also of mention from that same segment: Rachel's attempts to do ballet that end up with her hopping into the closet and knocking down a whole bunch of junk, her approaching the pool to learn how to swim covered with an inner tube, snorkel, and pool animals, and her attempts to play the piano. And sing.
The most clearly straight-up hilarious sequence is "Carnival of the Animals", with the yo-yo-obsessed flamingo and his peers who just won't get it.
Even before this: James Earl Jones: "Here, the sensitve strains of Impressionistic music combine with the subtle artistry of the animator to finally answer that age-old question...'what is man's relationship to nature?'" *is handed a sheet by an artist* "Oh, sorry. That age-old question 'what would happen if you gave a yo-yo to a flock of flamingoes?' Who wrote this?!"
In the DVD commentary (the one which talks about each segment), Donald came by. One of the guys complains why is Donald joining and he can't understand him. Donald brought the animals with him and the flooding waters. He told Donald they're doing a commentary not a reenactment. The commentary ends him asking where'd he parked the Ark.
Yen Sid giving Mickey a whap on the behind with the broom!
What makes it even better is if you pay close attention, Yen Sid betrays a little smirk right before he whaps Mickey, indicating that he thought the whole thing was Actually Pretty Funny.
The "soundtrack" line imitating instruments. Especially the bassoon— "drop the other shoe, will ya?" and the drums. (The triangle at the very end makes it art).
Roy Disney and Mickey Mouse chatting on the commentary to The Sorcerer's Apprentice, talking about costumes and Mickey falling down the stairs repeatedly, the Brooms Union, bringing in more brooms from Warner Bros., and not using a stunt double.
The Dance Of The Hours sequence with Expys from La Gioconda. Hyacinth Hippo is Laura, Madame Upanova is La Gioconda, and Ben Ali Gator is Enzo. The whole thing is just hilarious.
In The Rite of Spring, a pteradon snatches a squid from another pteradon, and he chases after them.
Later a little dinosaur was crawling to the dinosaurs that were digging. One pushed the little one as if saying "Beat it, kid. You're bothering me." Then, when they all looked up (as if they heard something coming), the little dinosaur snatched something from the hole and walked away.