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.
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.
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.
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.
Imagine the reactions if it goes to a fifth!
I bet on August 30th to be the day of the solution to the loop.
Also from Endless Eight: in the later loops, when Kyon gets a call late at night:
Kyon: (sleepy) Hello?
Kyon: Gah! * Juggles phone*
One thing that made the dubbed version of Endless Eight bearable was Kyon's even more awesome than usual dialogue:
(epic voice) "Restrain thyself! Dost thou not see the No Diving sign!?"
(sleepy) "The number you have tried to reach has been dis— Gah!" *Juggles phone*
"So, I come up behind Haruhi and say 'I lo— eeuuurgh'!"
(sipping Mikuru's tea) "It's strawberry-licious!"
"My turn! I summon my 'veto' card!"
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. 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.
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 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!
From Disappearance, Caterpillar-Haruhi.
Caterpillar-Haruhi falling over several times, no less.
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 bizaare events going on lately are completely logical? It Was All Just A Dream. (Beat.) "That wasn't a joke."