When Groose taunts Link about what happened to his Loftwing, you're given the option to taunt him back by saying, "nice hair." His reaction to that is priceless.
Groose (while pointing to his hair in annoyance): You lay off the do right now, or I'll flatten you. Everyone knows I've got the slickest pompadour in town.
Gorok the Goron states that he has been researching an ancient civilization related to the bird statues, or, more specifically, the "Isle of the Goddess" (Skyloft). Ask him what he knows, and he'll go on that since it was created by the Goddess herself, it must be a paradise where everyone lives in harmony, the trees are full of fruit that can cure any disease, the fields are full of pumpkins that never rot, magical wildflowers bloom everywhere, and that the weather's always perfect. He says these things to Link who had just come from Skyloft. Better yet, he reacts with amazement once Link approaches the bird statue... which reacts the same way to Link as what any other bird statue would if he were to approach them.
Much like in The Legend of Zelda: The Wind Waker, Link will be flung into the air and suffer a case of Rump Roast should he fall into lava. This wasn't too outlandish with Toon Link, but it's much funnier when the more realistic and serious adult Link has such a cartoonish reaction.
When you don't want to listen to a Sheikah Stone's advice a second time, it says the following quote:
Stone:Rumor has it you're some kind of genius that remembers things perfectly the first time you hear them...
Speaking of Sheikah Stones, try setting off a bomb near one. It randomly flies into the air like a rocket and explodes, then a new one grows out of the ground in its place.
The moment when Link learns the final part of the Song of The Hero. He's about to claim the harp and celebrate his victory when the music cuts off. Link's expression is totally worth it.
The scene after completing the Lanayru Mining Facility. Impa is fending off Ghirahim, and Zelda sends over the Goddess' Harp to Link. Suddenly one hears theItem Get theme as Link receives the Harp. Link's silly expression on his face probably helps as well.
He's also humming his own theme song while dancing.
If you don't fend off Ghirahim with your sword during the first and second fights, he attacks by pimp-slapping Link across the face.
How Zelda's Loftwing delivers her letter to Link: by spitting it at him!
After waking him up by screeching at him and causing him to fall out of bed.
And of course, the fact that Kleptomaniac Hero, among many, many other adventure-game tropes, are subverted throughout the course of the game.
One of the Gratitude Crystal sidequests also counts. It's a Mythology Gag centered around one of the weirdest Big Lipped Alligator Moments from Majora's Mask. To wit: you discover somebody in the Knight's Academy's bathroom in the middle of the night, crying out for paper ("any paper!"). When you find paper, she lets you into the bathroom... to reveal that it's a disembodied hand that appears from inside the toilet. The only thing that could make this better is the fact that the paper is actually a love letter. It's truly a thing of wonder.
If you analyze the hand, Fi assures you to "Cease being scared and talk to her".
One example is the first time you're exiting the basement floor via rope. Out of nowhere, the Cursed Bokoblins pop up and chase you up the rope, and if they catch you, you get to shake them off. It's hard to run away through the laughter.
According to Fi, the whole reason they cling to life is the attachment to their odd underwear.
Another moment from the Cistern basement is when you finally get the idol. A mob of Bokoblins springs from the ground and the statue above you begins to drop down from the ceiling/where it used to be the ceiling. You could probably stay to fight them all off, but it's infinitely more satisfying to sprint out of the way and watch the cinematic of them being squashed. And just for those budding PETM members: it's alright. They're already dead.
Bokoblins in general are Butt Monkeys in the Zelda series, but nowhere else is it more apparent than in this game.
Knocking them off ledges and watching them roll down the hills in Eldin, shaking them off the tightrope, stealing their monster horns with the whip and watching them pitch a mini temper tantrum over it, and all other forms of tormenting them are sadistically funny.
The cinematic after you insert the Stone of Trials. Link's blank expression practically screams "What."
This is likely a Call Back (or Call Forward) to a similar scene in The Wind Waker, where Link had a similar reaction to a very similar statue doing a very similar thing. Just that in The Wind Waker, Link went on to examine the statue closer in order to see if it's broken — only to have it blow up in his face.
When you start searching for Zelda in Faron Woods and come across a kikwi with her aura around it, answering "Zelda?" results in Fi giving an overly long analysis of the kikwi that confirms, with 95% accuracy, that the kikwi is not, in fact, Zelda. You know you've said something stupid when your swordstarts snarking at you.
Likewise, after the 2 Mogmas mentioned earlier on the page mention how a girl fitting Zelda's physical description to the letter was taken into the Earth Temple, you can suggest to Fi that it was actually Impa that they saw. By her calculations, the chances of that being true are '10%. Rounded up.'
If you repeatedly fail a Silent Realm trial, Fi eventually states that "the chances of you not being the chosen hero are increasing..."
When Fi assesses a fairy, she'll admit that there's a 10% chance it's actually an unknown species of insect.
Some monsters flee in terror at the sight of the beetle.
Which is actually smart of them on some level, such as with the boulder-tossing bokoblins on Eldin Volcano. It makes trying to get them to crush themselves with their own boulders a lot harder.
Drop a wasp hive on a monster. Laugh as they run around in circles swatting uselessly at their heads to try and stop the stinging.
Link's Item Get text when he receives the Sailcloth from Zelda and her subsequent reaction to either the pose or his fine print.
"... it smells nice too."
The very Ship Tease-ish scene with Link and Zelda on the Goddess statue during the ceremony. After she's done with her part, Zelda tells Link there's one final step to it, shyly asks him if he knows what that is (Link's answers are... nervously ambiguous), and then leans in extremely close to the point where she and Link's faces are mere inches apart... and then Zelda turns him around and pushes him off the statue.
Also note that this is the second time she pushed Link off from a dangerous height. On the same day. Makes you wonder if this is a regular thing between the two of them.
Afterward, you have to work for the owner to pay off the damages, but you can be a stubborn asshat about it every step of the way; trying to leave without even talking, refusing to do any work whenever he or Kina give you a job, drinking the Pumpkin Soup you're supposed to be delivering, deliberately playing the harp badly... All just to piss him off further.
If you get spotted in the stealth section of Eldin Volcano, a boulder will be launched on top of Link courtesy of some Bokoblins with a catapult, with the screen going black right before it hits him and a squishing noise.
If your sense of humor is dark enough, the boss fight with Koloktos — where you repeatedly chop its limbs off with its own sword and whale on its weak spot while it sits helplessly — can be Bloody Hilarious.
When you first fix Scrapper, he acts like a complete jerk. Then Fi comes out and he starts flirting with her. She's rendered speechless.
Scrapper: This individual may have restored me to operations, but I am not inclined to offer assistance. Serving children is very low in my task priority.
[Fi appears and gives a status update]
Scrapper: Who are you!? ZRRPT-FOOSH! Your name is...Fi? Should I call you Mistress Fi? Are you looking for something, Mistress Fi? I...I understand! At your request, I will carry anything, regardless of weight or destination!
At one point in the game, you need to learn the lyrics to the song Zelda was singing on the day of the ceremony. Headmaster Gaebora knows it, but states he'll just speak the lyrics rather than try to sing them. You can insist that he sing it, much to his sheepishness.
Falling in lava. It's like something out of a Mario game, complete with the hilarious yelling.
After the second Moldarach boss fight happens while you are searching for Skipper's ship, if you continue to search long enough, Fi will tell you that there is a 0% chance that the ship is there and that you should leave.
"Ah yes, the oral tradition. One of the least reliable methods of passing down information." Fi is just so hilariously matter-of-fact about how wrong Gaepora has gotten the prophecy.
The reaction the Stalfos have to getting caught in a bomb explosion. Their arms come off and they jerkily look left and right, as if they're incredulous about the whole situation.
If you throw a bomb at a Bokoblin, it'll run away. Do this with a Technoblin, and it may run right out of the Timeshift zone and turn into a pile of bones.
During the first fight with him, Ghirahim introduces himself saying that he prefers "his full title... LORD Ghirahim. But I'm not fussy." Link just sneers and waggles his head like "whoop-dee doo, aren't you special?"
The Guays/crows in the forest will sometimes poop on your shoulder. Link makes a horrified/disgusted face as he runs around with an adorable stylized poo on him.
Scanning them with Fi has her state that getting pooped on has a 100% chance of aggravation.
There's also something funny about how the poo drains your stamina gauge if left unchecked.
While battling Demise, Link can whip out his bug-catching net. Demise will actually pause to stare at it.