After Kirito and Asuna meet for the first time, she borrows the bath in his rented room. Kirito's reaction to the idea of Asuna in the bath:
"I didn't know averting my eyes from that door required such a high will saving throw."
When Argo knocks on his door, Kirito knows this is going to end badly. His first instinct is to flee.
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.
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.
Kirito learns that (most of) his SAO skills carried over to ALfheim Online. When he learns that he needs to delete all the incompatible items that also got carried over so he doesn't get attention from the Game Master, he struggles to press Delete. Think about it for a second. Kirito is forced to erase all his hard-earned loot, something dedicated players of other games wouldn't even dare to do that easily.
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.
Kirito getting surrounded by two beautiful women and making him uncomfortable is funny in itself, until you look closely at Kirito's left-breast pocket◊.
Related: Sakuya and Alicia vamping it up in the English dub of the anime.
At Agil's party, Kirito orders a bourbon on the rocks. Agil hands him a glass, but then Kirito says, "What gives? This is oolong tea!" Sorry Kirito, you may be the hero of SAO, but you're still only 16.
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 noodles 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.
At the conclusion of Caliber, after Shino succeeds in retrieving Excalibur for Kirito, she turns to him, presents the sword with a big smile, and says, "Please think of me every time you draw this sword." Kirito can feel the Death Glares from his harem.
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».
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!!
After the players real looks are exposed on their avatars, a beautiful couple that we saw earlier are actually revealed to be two older guys. Their reaction is priceless:
"Pretty Guy":You're a guy? "Pretty Girl":You were lying about being seventeen?
In Episode 4, Kirito knocks on Silica's bedroom door, and she nearly answers the door while in her underwear.
In Episode 10, while Kirito and Asuna are at Asuna's house, Asuna strips down to her underwear and tells Kirito to get undressed as well. When a flustered Kirito says that wasn't what he meant when he said he wanted to spend the night with her, Asuna punches him out. With a Sword Skill.
The Gratuitous English lines the cowboy was spouting out were funny as well. "I'll kill you!" "You loser!" "Die!" "Go to hell!"
Episode 5, Season 2: Sinon, still thinking Kirito is a girl, has no problem with being only in her underwear. When confused by Kirito freaking out, he then reveals his true gender, much to her shock ("Male!? You're a guy? With that avatar!?")... then the inevitable situation slowly dawns on her. Kirito gets slapped for his troubles, leaving a hand print on his face that looks awfully familiar.
After this, Kirito follows Sinon around, and she acts like he's stalking her.
Later, while Kirito starts being annoying while Spiegel is around, he uses his "girly" voice, making the scene even funnier.
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.
Episode Guesting Yui: "I have a question: Mama says she wants to have lots of kids with Papa. Uncle Klein, how exactly are babies made?"
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's opinion.
Asuna: W-W-Well Yui-chan, first you have to go down the menu and turn off the 'Ethics Code', and then— Kirito:S-S-Stop right there! We can't teach her that! Y-Yui, the truth is, when a couple gets married, a stork brings the baby! Yui: S-So, I, I'm not Mama and Papa's daughter??
The manga 4koma omakes. Most — if not all — of them. There's a lot of Notable mentions :
The many many back stories before Kirito met with his friends such as how Lizbeth gets her house and outfit in the first place and Leafa and Recon's first encounter.
Anything with Asu-nyan. And no it is not Azusa from K-On!!
The next 4koma scene Kirito brought up the catgirl shopgirl when Asuna suggest to find a blacksmith. Cue to Asuna nearly stabbing him.
Ironically, one of the 4koma shows Asuna in a sexy succubus outfit. Lizbeth loves to cosplay people.
Kline's encounter with a nekama (a guy pretending to be a girl on the internet) and cue to how the end results.
The main reason why Agil's shop never sell his stuffs well? He was making deals...when he's asleep.
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:
It turns out that Kirito requested Asuna to do a Cat Girl cosplay of the outfit made by Lizbeth instead.
Sword Art Online Extra Edition contains hilarious scenes where Rika/Lizbeth lampshades stuff, namely: Keiko/Silica looks nothing like Suguha (especially in the chest), Kirito and Asuna having sex in SAO, and Suguha's more than familial feelings for Kirito. Everyone gets very defensive when these things are brought up.