Each time Kyon Squees over Mikuru is funny. "SO CUTE!"
The Nonindicative First Episode is hilarious, but a particularly good scene from it is when Kyon's pet cat starts talking (in a manly voice, to boot, despite being a calico) and you can hear Kyon shouting off-screen for it to stop. Yuki bops the cat on the head with her "magic wand" and "explains" in a complete dead pan that she was using ventriloquism.
Speaking of which, right after Haruhi granted it with the ability to talk, Kyon's conversation with the said cat suddenly becomes a deeply insightful philosophising on how beings communicate to each other with futility. Hilarity ensues.
Koizumi: You know he's got a point...
Kyon: No, the cat does not have a point!
Mikuru firing a gun is also pretty funny as is the conspicuous Male Gaze.
Not anymore! Sighs was finally adapted to anime in season 2.
Kyon's adlib during the Koizumi/Asahina Almost Kiss scene:
Kyon: If your mouth gets any closer to her, someone standing off camera is gonna step into frame and kick yourass, dammit!
Kyon's narration after the break when Mikuru was changing clothes
Kyon: We didn't film her so don't bother asking for the footage, there isn't any.
And it's funnier because, knowing Kyon, he's probably lying.
Kyon trying to figure out plot details.
Kyon: Aaaaand... when in doubt, pan to the left.
Kyon's flabbergasted reaction after watching the film is just PRICELESS.
Part I: Kyon's first meeting with Mikuru when Haruhi demonstrates one of the reasons she was chosen by groping her from behind. Mikuru's whimpering only makes it funnier, no matter how wrong that sounds. Of course, Your Mileage May Vary, but it was the first scene where this troper burst into laughter.
Made even funnier by the fact that in the novels, she actually says "I'll just say you guys gang-raped her!"
But in the anime, there is at least one other word that can fit the bleep, and it starts with an "f".
The dub has superb bloopers and delivery thanks to the English cast just being that good.Crispin Freeman in particular can do great ad-libbing, which is perfect for a sarcastic Unreliable Narrator. His various takes on the same line is one of the saving graces of Endless Eight.
From the same episode, Kyon guessing that Haruhi's... weird signals... are an attempt to lower the opposing team's "magic points".
If you're listening to the conversations in the background during Haruhi and Kyon's discussion on team order, you can hear an interesting story about how Taniguchi and Kunikida became friends...
Also: "I've dishonored my family..." * hangs head in shame*
The Beach Episode had this troper snickering when they were playing with a beach ball in the water. Mikuru hits it into the air, and while several people are going to catch it, Kyon exclaims (in his head) "Too many beach balls!"
Setting up the third Endless Eight episode to be the end of the Groundhog Day Loop only to end it with nothing resolved leaving it to a fourth episode. Not particularly funny in the show but the reactions of people watching seems to have cemented Kyoani's Kadokawa's status as master level trolls.
Also, Itsuki's explanation of what's going on in the third "Endless Eight" episode:
Itsuki: "We've entered an endless recursion of time."
Hell, the one time his phone rings his only response is a screaming fit of Angrish
The opening scene of episode 10 in the new season. SOS Brigade sign suddenly moving at impossible speeds during a relay race? It's Yuki. Even Haruhi has trouble believing her eyes. Koizumi's mention about the track team's likely broken spirit (as they're seen walking past behind him) makes it all the more funny.
While not mentioned much in the anime, it becomes a plot point later in the novels that the SOS Brigade was never recognized as an official club. So they shouldn't even be racing. Which makes this even funnier.
In "Live Alive," the shot of Kyon rocking out to "Lost My Music" in impeccable Deadpan Snarker style.
From the same episode, the look on Taniguchi's face upon seeing Mikuru in her maid outfit.
In one scene, whilst Kyon is monologing, a bratty kid screams at a man in a teddy bear outfit for giving him a non-red balloon. His mother's response - "Shut up or I'll leave you here!"
In the episode "Someday in the Rain," Every instance of Yuki 'convinently' blocking the camera view everytime Haruhi strips Mikuru.
From the dub:
Haruhi: This is so~ fun! Takin' all your clothes off!
Kyon: *small-wave* "Hey" ; Itsuki facepalms in the background at this
From Disappearance, Caterpillar-Haruhi.
Caterpillar-Haruhi falling over several times, no less.
Haruhi: Let me know when your gonna wake up BEFORE you wake up!
Also from Disappearance: the opening musical-credit sequence, with (dialogue-free) shots of Kyon warming up in front of the heater. Then, one by one, the rest of the SOS Brigade start jostling for room...and by the end, the pecking order is firmly established, with Kyon reduced to trying to warm himself by the computer.
Having just found Alt!Haruhi, Kyon now has to bring her to the Literature club room but has to get Haruhi to somehow disguise herself. After only a second of hesitation, he calmly asks her to put her Rapunzel Hair into a ponytail. Cue audience laughter.
The way Taniguchi turning down Kyon's invitation to the SOS Christmas party is hilarious in hindsight when it's later revealed that
His girlfriend is Kyou Sou. Who mistook him for Kyon.
From "Editor in Chief": Mikuru walks in on Haruhi sitting on top of prone Kyon, trying to rip off his jacket, jumps to the obvious conclusion, and runs away shouting apologies.
The Sigh of Haruhi Suzumiya, part five, in the anime. Itsuki's proposal to convince Haruhi the bizarre events going on lately are completely logical?
Itsuki: There is one ending that can explain any nonsensical plot...that can wrap up every little detail with ease. Kyon: Well? Let's hear it. Itsuki:It Was All Just A Dream. (everyone stares at him) Itsuki: I'm not kidding, that's the ending I was talking about.
A minor one, but the English translation of the fifth novel has Tsuruya address Haruhi as "Harls".
In Intrigues, Tsuruya spouting off innuendo at Kyon every time he shows up at her house to check on Mikiru.
In Surprise, Kyon has to go back to the clubroom to meet with Yasumi, and he needs an excuse to say to Haruhi. So he tells her, to her face, that Taniguchi had lent him a rare porno magazine, and there'd be big trouble if it were discovered in his desk. Haruhi is left speechless.
Some of Kyon's narrations are pretty damn funny, especially his "No, but my danger sense was tingling." after Haruhi stares at him.
Yuki rarely plays jokes, but when they happen, they are subtle and pretty funny if you realize it
In Melancholy after Haruki and Asahina change into the bunny-girl costumes for the first time she makes Kyon pick up the discarded cloths and undergarments.
In Remote Island Syndrome, her literal interpretation of Haruhi's orders about the door counts.
Kyon: Maybe that was Nagato's way of playing a joke on us.
Her explanations during the Mikuru Beam incident also count as a deliberate joke. She stretches it waaaay out. And her pedantic corrections of Kyon make this entire scene hilarious.
Kyon: Was Asahina seriously firing beams from her eyes?
Yuki: Not a particle projection cannon. Concentrated light.
Kyon: The problem we have here is that Asahina has been shooting off heat rays.
Yuki: Not heat rays. Photon laser.
One from the second episode of the Sigh of Haruhi Suzumiya in the anime counts as a Funny Background Event. An unseen kid asks their mother while the SOS Brigade are shooting a commercial, 'Momma, what's that?'. His mother's response? 'Sssh. Those are crazy people.'. Kyon's embarrassed reaction makes the moment priceless.
The scene where we find out where Haruhi plans to get funds: Take it from the Literary Club budget.