The entire first chapter. The Muggle Prime Minister's reaction to Fudge and his antics is absolutely hilarious.
Especially funny when you realize that the Muggle Prime Minister at the time was John Major. Or, in other words, the least funny, greyest man not just in British politics but those of any other country, the man who ran away from the circus to become an accountant, whose most charismatic moment was squeeing at his old concrete house in Birmingham, is now having a conversation with the Minister of Magic.
Fudge mentions that the Prime Minister's predecessor tried to throw him out a window. Major's predecessor was Margaret Thatcher. It's something you can actually imagine the Iron Lady doing, and it's great if you do.
Snape's retort about Ron's Apparition failures isn't bad either.
Gryffindor's second Quidditch match. In layman's terms: Gryffindor's goalkeeper tries to teach the Beater (who hits cast-iron balls called Bludgers at other players) how to play his position, inadvertently using Harry as his object of demonstration. He wakes up hours later in the Hospital Wing, with a cracked skull. Madam Pomfrey mends it at once with a spell, but:
Madam Pomfrey: I'm keeping you in overnight. You shouldn't over exert yourself for a few hours. Harry: I don't want to stay here overnight, I want to find McLaggen and kill him. Madam Pomfrey: I'm afraid that would come under the heading of "over-exertion".
Also on McLaggen,
Ron: Final score: Three-hundred-and-twenty to... sixty.
Then shortly afterward Ron casually mentions that Ginny had stopped by while Harry was unconscious. "Harry's imagination immediately went into overdrive, swiftly constructing a scene in which a tearful Ginny confessed her feelings of deep attraction while Ron gave them his blessing..." Only to have it implode when Ron mentions she was just wondering why he was so late for the match. You can almost hear the Record Needle Scratch.
"But the more I hint I want to finish it, the tighter she holds on. It's like going out with the giant squid."
Try not to laugh when Hagrid and Slughorn get hammered and start singing a sad song. You will fail.
Slughorn:And Odo the hero, they bore him back home, to the place that he knew as a lad, they laid him to rest with his hat inside out, and his wand snapped in two, which was sad. Hagrid:(about how good people die young) ...terrible. Slughorn: Sorry. Can't carry a tune to save my life.
"We're not going to be asking, 'Excuse me, are you the imprint of a departed soul?'"
What about the "Roonil Wazlib" scene?
Snape: This is your book? Harry: Yeah. Snape: Then why does it has "Roonil Wazlib" in it? Harry:(beat) That's my nickname. Snape: Your nickname. Harry: That's what my friends call me. Snape: I understand what a nickname is.
Peeves blocking a hallway and claiming he won't allow anyone to go through unless they set their pants on fire. Harry and Ron just take a different route. Five minutes later, Neville comes in, smoking and looking for a pair of pants to change into.
Ron diving behind Hermione everytime he thinks Lavender is passing by: "Hide me!"
Harry's method of getting rid of Goyle when Goyle's disguised via polyjuice potion as a little girl while standing watch for Malfoy: to walk up behind him/her and go: "Hello... you're very pretty, aren't you?" prompting Goyle to run away screaming.
The students first seeing the love potion and how they just, sort of, float toward it.
"Yes, Harry Potter! And if Dobby does it note (stalking Malfoy) wrong, Dobby will throw himself off the topmost tower, Harry Potter!"
Which becomes a "Funny Aneurysm" Moment, considering someone does get thrown off the topmost tower at book's end...
Later, while reporting on said job:
Dobby: (proudly, swaying where he stands) "Dobby has not slept for a week, sir!"
Hermione: (gives Harry a scandalized look).
The sign outside Weasleys' Wizard Wheezes.
"WHY ARE YOU WORRYING ABOUT YOU-KNOW-WHO?
YOU SHOULD BE WORRYING ABOUT U-NO-POO
THE CONSTIPATION SENSATION THAT'S GRIPPING THE NATION!"
Especially Molly's initial (nonverbal) reaction of complete disbelief.
The almighty Peeves can always be counted on for a good laugh.
"Bitey, scratchy, pokey, draw his cork and pulls his earsy"
"Where there's strife and when there's trouble
Call on Peevsie he'll make double!"
After Harry drinks the Felix Felicis, and acts like he's high.
Hermione: This is Felix Felicis, I suppose? You don't have another bottle of. . .
Harry's pining after Ginny results in a lot of these:
"It was natural that he would be concerned about her. Natural that he would want to look after her. Natural that he would want to blast Dean into a million pieces for kissing her...no, he would have to control that particular brotherly instinct."
"Ginny kept popping up his dreams in ways that made him devoutly thankful that Ron couldn't perform Legilimency."
Snape's deliberate tweaking of Bellatrix in the second chapter, where he answers all her suspicions about his loyalty, while almost constantly insulting her:
Snape: "Of course you weren't a lot of use to him [in Azkaban], but the gesture was undoubtedly fine."
Luna Lovegood meets Professor Trelawny. Luna starts telling her about the "Rotfang Conspiracy" (the non-existent aurors' plan to bring down the Ministry of Magic by using "a combination of Dark Magic and gum disease"); Trelawny is genuinely fascinated.
When Fleur at first tells Mrs. Weasley that Bill will still love her after he was attacked by Greyback, and then when she does understand what Mrs. Weasley was inferring raves about how she doesn't care about how Bill looks and that she's "Good looking enough for the both of them!"
A small one during Dumbledore's funeral when Umbridge sees Firenze and immediately books it to a seat as far away from him as possible.
Another small gem: Kreacher sends Harry a Christmas present while he's away at the Burrow. It's a package full of maggots.
From the film:
After Luna fixes Harry's broken nose:
Harry: How do I look? Luna: Exceptionally ordinary.
Harry: Oh sir I really think I should get back to the party. My date...
Snape: ...could surely survive your absence another minute or two.
And Snape probably knew (either through Legilimency or just because he's Snape) that Luna was Harry's date - and, more than likely, he was absolutely right.
Hermione trying to duck her date, who she only brought because she thought it would annoy Ron. Her Adorkable actions are priceless.
Ron spotting his sister making out with Dean Thomas:
Ron: I'd like to go home now.
Hermione's butterbeer mustache and her startled hare-type reaction followed by a Longing Look when Ron just as awkwardly points it out. It's like she's saying "Great, he failed to get my hint about us snogging and now I'm embarrassing myself."
Prof. Slughorn: Harry?! Harry:(same annoyed tone) Sir?!
Harry during the whole Felix Felicis scene is complete funny awesomeness. Harry, with his uncharacteristically peppy attitude, steals the entire scene (especially when he enacts how a giant spider's pincers work).
Seriously, Google "not to mention the pincers" on images. There's a bunch of them. And, it's hysterical.
The whole bit with Slughorn sneakily cutting a leaf from a plant in the greenhouse when Harry walking into frame in the background, turning and seeing him and getting right next to him without saying anything and Slughorn getting the crap scared out of him when he turns his head.
Right after taking the Potion, Harry's alarmingly happy "HI!" to a random dude.
There might be an interview somewhere, where Dan said that he enjoyed doing the Felix Felicis scenes because instead of acting like Harry, he simply had to act like himself.
Hermione: I think she's trying to smuggle you a Love Potion. Harry: Really? (smiles at her) Hermione: She's only interested in you because she thinks you're The Chosen One! Harry: But IamThe Chosen One. (Hermione slaps Harry upside the head) Harry: Sorry. Don't worry, I'll take someone I like. Someone cool. (hard cut to Luna)
Ron under the love potion. All of it. Ron staring at the moon when he was under Romilda Vane's love charm:
Ron: It's beautiful, isn't it? The moon. Harry: Divine. Had ourselves a little late night snack, did we? Ron: It was on your bed, the box, I just thought I'd try one. Harry: Or twenty. Ron: I can't stop thinking about her, Harry. Harry: Honestly, you know, I reckon she was starting to annoy you. Ron: She could never annoy me. I think I love her. Harry: Oh... brilliant. Ron: Do you think she knows I exist? Harry: Well, I'd bloody well hope so, she's been snogging you for three months. Ron: Snogging? Who are you talking about? Harry: Who are you talking about? Ron: Romilda, of course. Romilda Vane. Harry: Okay, very funny. Ron:(throws the chocolates box at Harry) Harry: What was that for? Ron: It's no joke! I'm in love with her! Harry: Alright, fine, you're in love with her! Have you ever actually met her? Ron: No... Can you introduce me?
The bit where Snape tells Harry that Dumbledore has had to go, and when Harry asks where, Snape just looks at him for a moment and walks off. Perfect comedic timing.
McLaggen flirting with Hermoine. By licking his fingers.
Harry coming back to the feast after being sneak attacked by Malfoy.
One of these lines is said by Ginny, which (given her previous experiences) makes it borderline Black Comedy.
Then there's McGonagall's exasperated "Why is it always you three?" upon discovering Harry, Ron, and Hermione are caught up in the crisis du jour yet again. And Ron's reply, for that matter.
McGonagall:(to Harry, Ron, and Hermione) Why is it that, whenever anything happens, it's always you three? Ron: I've been wondering that myself for six years, Professor.
Price negotiations with Fred and George.
Ron: How much are these? Fred and George: Five galleons. Ron: How much for me? Fred and George: Five galleons. Ron: I'm your brother. (beat) Fred and George:Ten galleons.
Also, Fred and George each have different expressions when they say that last line, both funny.
Weasleys' Wizard Wheezes shop features an animated doll of Umbridge skating across a tightrope, squealing "I will have order! I will have order!" Let us hope there was a spiked pit under it and the doll was incinerated if you tipped it in.
When Harry and Dumbledore are about to leave for the cave:
Harry: But sir, I thought you couldn't Apparate in Hogwarts. Dumbledore: Well, being me definitely has its advantages.
The scene where Ron is in the hospital wing after being poisoned, and his annoying girlfriend Lavender comes in worried and asking "Where's my Won-Won?" She and Hermione get into a fight over him, where Hermione calls her a "daft dimbo"! What makes this even funnier is that it's happening in front of the teachers — Dumbledore, McGonagall, Slughorn, and Snape. Then Ron calls out Hermione's name in his sleep, and Lavender runs off crying; Dumbledore quips "Oh to be young and to feel love's keen sting!"
Dumbledore delivers that last line in the most airy, cheerful manner possible, like he didn't just witness an angsty teenage romance drama... or like he's seen similar scenes so many times during his years at Hogwarts that he's no longer fazed by them.
Also the way that Snape just stares straight ahead during that scene. And the fact that he's there at all watching it. It also becomes a little funny and sad once you realize that he should know how Lavender feels.
When Dumbledore mentions Harry's quick thinking using the Bezoar to counteract the poison, Snape shoots Harry a highly surprised look, clearly seeming to wonder, "Did Potter actually remember somethingI taught him?"
A rather subtle one, but Slughorn's face sports a quick "Oh, Crap" look when he accidentally rips off Aragog's pincer while trying to extract some of his venom? Right in front of a sobbing Hagrid, by the way.
After Harry and Ginny's first kiss in the Room of Requirement, Ron's line in the very next scene;