"Uncle Vernon made another funny noise, like a mouse being trodden on."
From the Stephen Fry audiobook, the sound he makes when Harry steps on Vernon's face as he's camping by the front door.
After Ron meets Hermione for the first time, he comments, "Whatever House I'm in, I hope she's not in it." Of course, not only does Hermione end up in Gryffindor with him, but the epilogue in the seventh book reveals that she eventually becomes his wife, meaning that Ron will live in the same house as Hermione for the rest of their lives!
Dumbledore's pre-banquet speech:
"Welcome! Welcome to a new year at Hogwarts! Before we begin our banquet, I would like to say a few words. And here they are: Nitwit! Blubber! Oddment! Tweak! Thank you!"
It's a small one, but nonetheless the scene where Hagrid is in Gringotts and reaches into his pocket to find Harry's key only to come up with a bunch of dog biscuits counts.
Made even funnier when you realise that those biscuits are meant for Fluffy; i.e., a giant three-headed monster dog.
The Weasley Twins at the beginning.
"Don't cry, Ginny. We'll send you loads of owls.—"
"We'll send you a Hogwarts toilet seat!"
"Only joking, Mum."
Even funnier is that it's a callback to an earlier funny moment. Mrs. Weasley makes it clear that she wants the twins to behave this year, leading to her warning them "If I get one owl that you've... blown up a toilet or something..." This cues them to respond that they've never done that before, and are grateful for the suggestion.
Dumbledore: "I believe your friends Misters Fred and George Weasley were responsible for trying to send you a lavatory seat. No doubt they thought it would amuse you. Madam Pomfrey, however, thought it might not be very hygienic, and confiscated it."
More from the hospital wing scene:
"What happened between you and Professor Quirrell down in the dungeon is a complete secret, so, naturally, the whole school knows."
After Hagrid tells Harry and Hermione that he's given Norbert a teddy bear:
From inside the crate came ripping noises that sounded to Harry as though the teddy was having his head torn off.
Realizing that in the first book, Fred and George jinxed snowballs to hit Quirrell's turban, and that they were unknowingly smacking Voldemort in the face!! You can just imagine Voldemort under the turban going "don't blow your cover, don't blow your cover, don't blow your—" *SMACK*
Dumbledore's Chocolate Frog card: "Professor Dumbledore enjoys chamber music and ten pin bowling." Best. Mental. Image. Ever.
Jim Dale singing "Hoggy Warty Hogwarts" for the audiobook of Philosopher's Stone.
"While he drove, Uncle Vernon complained to Aunt Petunia. He liked to complain about things: people at work, Harry, the council, Harry, the bank, and Harry were just a few of his favorite subjects. This morning, it was motorcycles."
When Harry gets the idea to have Charlie Weasley take Norbert off of their hands, he first launches the idea by glancing at Ron and muttering "Charlie". Ron's response?
"Now you're losing it too. I'm Ron, remember?"
Harry tells Ron and Hermione that Snape is going to be the referee for the following match.
Hermione during the flying lesson, when Harry persists in chasing after Malfoy: "What. An. Idiot."
The Sorting Hat scene. When Dumbledore announces that the third-floor corridor is out-of-bounds to anyone who "does not wish to die a most painful death" (and does so in the same businesslike way he handles all of the other announcements), the other students whisper amongst each other in curiosity. Meanwhile, Harry's face is pure WTF. It's #1 on this list.