In regards to Kirito's hairstyle in Caliber side story :
A little fairy flew from Asuna's shoulder—she was a Navigation Pixie named Yui, landed on my head and sat down. My Avatar, the Spriggan «Kirito», had long pointed hair, at Yui's request now I have my old hairstyle. The reason was it was «hard to sit on».
The first time Klein and Asuna meet, he immediately regresses from being a confident swordsman and leader into a nervous wreck. And then is annoyed that Kirito is in a party and practically on a date with Asuna.
And then he asks Asuna to treat Kirito well, even though he's not very good with words, isn't very fun and battle-obsessed. The reactions are what cross the line. Asuna's declaration: "Please leave him to me!" Kirito's response is to run away.
In Volume 7, a while after Kirito arrives to Hold the Line against an entire guild so Asuna and the Sleeping Knights can take on the floor's boss, Klein also shows up behind said guild to assist Kirito. Then we have this hilarious exchange between Klein and Kirito, shouting at each other from across the room.
Klein:"UWOOOAAAAAAHHH!!! I'M HERE TOO, EVEN THOUGH YOU CAN'T SEE ME!!!"
Kirito:"TOO SLOW! WHAT IN THE WORLD WERE YOU DOING!?"
Klein:"SORRY, I GOT LOST!!"
Kirito's reaction to people crowding over the duel between him and Heathcliff in the novel :
"...Let's run away Asuna. We can go live in some small village on the 20th floor and plow fields."
Possibly more amusing than just funny, but it's great for Kirito that his title changed from "The Black Swordsman" to "The Dual Wielding Demon" shortly before he was forced to join Asuna's guild (because her guild leader thought he was stealing her from them and was against it) and don a white outfit.
In a side story A Murder Case in the Area, Kirito and Asuna invite Heathcliff over for a meal to ask some question. Problem aside, the noodle they tasted are so bad that Heathcliff or rather, Akihiko Kayaba, THE CREATOR OF SAOOF ALL PEOPLE even wonder why the shop exist!
For fans who don't regard it as Squick, Chapter 16.5 (in which Kirito and Asuna have sex) is rather hilarious... for all the wrong reasons. It's very badly written in comparison to the rest of the story - Kirito's narration is consistently ridiculous (with phrases like "two years of semen" and "glopping sound" being thrown around) to the point that it seems like a Self-Parody, Asuna climaxes an impossible number of times, female genitals apparently look extremely silly (like white foam) in the SAO world... You either pretend it didn't happen or accept that it did and laugh the whole way through.
Or you can imagine it as the sex scene from the first Scary Movie.
Two years of semen (assuming the system saves the data on it as specific units, unlike the inconsistent patterns of real humans) = roughly a gallon. Try that mental picture on for size and try not to fall out of your seat giggling like an idiot.
After Kirito straight-up destroys a Salamander raid team aimed at his head with the Beast Form spell, Leafa has a moment of Fridge Horror when she realized Kirito basically ate some of them. Cue Kirito teasingly chomping down on her hand, and getting smacked for it.
Winning moments of the DVD commentaries are the Playback Corner segments and Life Counseling (a la Oreimo) parts. To name a few examples:
News Headline (Volume 1, Episode 1): The headline states that a lot of "girl players" revealed their true forms once Kayaba's revelation was unveiled. "This event only proves further," Asuna reports, "that there are nogirls on the Internet." Kirito mentions that the trend of playing as the opposite gender is rather popular with players recently. Cue Asunaimagining a genderbentprincess Kirito needing rescue from a prince Asuna.
Yui's Offline episode is especially amusing. Continuing on the quote above, Klein has been accused multiple times by Asuna and Kirito of teaching Yui "improper things" and he has to answer honestly. He asks for Asuna'sopinion.
Asuna:"W-W-Well Yui-chan, first you have to go down the menu and turn off the 'Ethics Code', and then—"
In a rather ironic aversion of the anime commentary in Yui's episode, the manga omakes reveal that (in that continuity) Yui was observing Asuna and Kirito's behavior from the start. Everything. Possibly including, yes, friggin 16.5. To quote:
Asuna said that marriage is pragmatic in SAO. Kirito thought she said plastic.
During the last day of their honeymoon, Kirito and Asuna agree to help an old player with a rare fishing based monster spawn. While Kirito is reeling in, everyone else flees a couple hundred yards when they realize how massive it is. When Kirito looks up to see the hulking monster climbing onto land, he takes off like a bullet, cowering behind Asuna and complaining about how his wife ran away and left him to die.