Kyon: Big Damn Hero/Funny

"Bad Ryouko! No class rep votes for you!"
When Yuki first starts managing Haruhi's powers she informs Kyon a long list of requests that need his approval. This interchange culminates in:

Yuki: Program nine goal: Enlarge Suzumiya Haruhi's--
Haruhi: Yuki, that's enough! Just forget, um, all of them! And forget about that one especially! You can't say that kind of thing in front of Kyon!

Hanyuu and Yuki's encounter in the bath. Each believes the other to have unfriendly intentions towards Kyon (who they're both playing "invisible spirit guardian" for the moment) and nearly come to blows... and then Kyon abruptly stands up and starts looking for a towel. Both girls immediately stop fighting and just STARE for a minute or two.

Hanyuu: We have just shared a wonderful experience. We should use this opportunity to become friends.

Kyon annoys himself sometimes.

"Well... 'future me' is a bit arrogant and constantly thinks that he can talk down to me just because he's been through whatever," Kyon sighed. "While past me is in fact incompetent, and I'd never go back to save him if he hadn't messed up in the first place. Present me, naturally, is just perfect."

In Fanservice Chapter 4 Mikuru was starting to complain to Haruhi because she was talking with Tsuruya while leaving her in the dark, until Haruhi shows her a picture of Kyon wearing an apron.

Mikuru: That's not fair! What do you think- *squee*

Mikuru telling Kanae to run and save herself because... Haruhi had just started nuzzling Mikuru's neck and expressed a desire to take Kanae home with her.
In Thwarted Lull Chapter 1. Mikuru giving Kyon the "it's forbidden" speech... while all but wrapping her body around his as she tries to kiss him with utmost desperation, following a "cuteness overload".
Haruhi's slide show presentation to the student council in defense of Kyon.

Haruhi: I would have thought you were too old for character-print underwear, Kimidori-chan. You should come to my club, sometime, though, Kanae-chan is a big fan of Trope-tan, too!

Kyon's parents are chewing him out for his involvement in the violence at school...and then Tsuruya and her father show up, the latter thanking Kyon for everything he's done for them.
- Later in the same chapter...

Yuki: At this juncture, I will attempt to communicate something to you, though I am uncertain as to the accuracy of the transmission. Words remain a weak vector for communicating vital information. Despite the lack of adherence to social norms and the correct protocols for this procedure, I am attempting to convey to you the positive emotive content of my current condition and regards for you. The outcome is uncertain; no accurate prediction can be made. Regardless of the fact that determination is unclear, I have resolved to continue due to the content of the emotive concept I wish to relay. Despite the fact that I have no comparable metric, I am currently unable to conceive a greater intensity than the one I experience at this moment in relation to you.

*Beat*

Yuki: I attempted to use more words. It appears that the data was not conveyed accurately.

Kyon: C...can you try it again with less, maybe?

Yuki: Yes. I like you. A lot.

"Crazy Asakura bits". 'nuff said.
- Tsuruya's line after the aforementioned crazy Asakura bits get turned into the PDA, Skynet is priceless.

Is that the end of the world in your pockets, or are you just happy to see us?

In Calm Before the Storm chapter 2, Kyon calls Yuki by her given name for the first time in front of all brigade members, cueing her first unmistakable Luminescent Blush. The event even warranted interference from future to ensure the moment was properly recorded.

Haruhi (to Kyon): Did you, or did you not just see the most amazing explosion of moe within this room ever just now?

In Storm Begins 2, Haruhi's sheer incredulity at Kyon's sincere attempts to undo the Tenchi Solution are nothing short of hilarious.

Haruhi: And, come to think of it ... you're a guy! What is wrong with you that you're trying to get out of a relationship with five attractive women?

In The Storm Begins, Chapter 2, Koizumi shows himself to be a Rena-sensei fanboy (Brave Detective Sasha Fan-club, member #24601) when Kyon reveals that she's his aunt, and Squees over the prospect of meeting her.

"Kyon," Koizumi said with unexpected heat in his voice, "I don't know that I've ever asked for much as a personal favor - but please let me meet your aunt!"

ACHAKURA.
- Especially when Yuki backhands the chibi across the room.
- Also,

"She is no longer dangerous." Yuki's gaze was fixed on Ryouko, still.
"W...wah!" Ryouko yelped. "Yuki-chama's eyes are cold!"

From The Storm Begins, Chapter 4, we have Rena's reaction upon seeing Yuki cosplaying as her novel's protagonist.
Koizumi's reactions to the sensations he's receiving through his link with Haruhi in Chapter 29, while Haruhi and Kyon are making out in the stairwell, are nothing short of priceless. Zoning out randomly, acting hilariously flustered, and finally delivering this gem of a line under his breath when the pair stops:

Koizumi: Thank the gods, they're finally done.

Open Battle Chapter 7. The contents of Kanae's "private" sketchbooks are revealed.
Asakura's pure logic take on BL H-Doujinshi.

"I understand that human males experience a lot of urges like that at Kyon-kun and Koizumi-kun's age," the figure replied, giving a solemn nod. "So it makes perfect sense that they would work together to get rid of them instead of spending time trying to get females to help!"

After Yuki hugs Kyon to buy Haruhi time to mess with Kyon's PDA:

Haruhi: Er, er, good work. Um, more emotion next time, Yuki, and then we'll have that sequel down solidly!
Yuki: Good.
Haruhi: That means you can let go!
Yuki: Understood.
Haruhi: That means let go!

Laying Low Chapter 4 gave us Tanaka Taro, the thug with ambition and a completely forgettable name. Let us not forget his final line in the chapter:

He was nothing, if not an ambitious man. From dockworker to management ... he would follow this path and truly achieve greatness in the shipping industry!