Wolf Link stands fiercely at the entrance of the deserted town at high noon. Sweeping camera angles and quick cuts map out the area and display the many cats that now infest it. Then the spaghetti western music cues, and you know that Link is going to befriend the hell out of them.
Midna is a veritable vending machine full of these. It helps that she's the game's resident Deadpan Snarker, too. One quote in particular jumps to mind:
Midna: There isn't a nicer way to collect [the light bugs] than to burn someone's house down, is there? Oh well. I guess that's just the way the cookie crumbles.
Another one, in a nice case of either Lampshading or some Fourth Wall Trope:
Midna:You're just now figuring out where Zant got his power?
There's also her antics with the sword and shield once you go into the Twilight for the second time. She tries to hold the sword by the blade, and wears the shield like a mask.
"Say something. Am I so beautiful that you've no words left?"
If you find the bridge that goes to Kakariko Gorge, or the missing piece of the Eldin Bridge, but teleport to the wrong place, you may get this gem (among others possible):
Midna: Hey! Are you doing that on purpose to make me mad?! Are you trying to drive me crazy, bringing me to a place like this?! Give me a break!
In another case of in-game lampshading, when you enter the Lakebed Temple, she says that it's a much better place that the Goron Mines. As you make your way through the temple, her opinion changes from enthusiastic to annoyed.
Midna: Why did those Zoras think it was a good idea to build such a huge temple?!
Whenever Link turns into a wolf, she gets on his back quite abruptly...every single time. The annoyed growl and look he gives her are quite amusing.
Right before she transforms after using the Fused Shadows, she is flung against the wall a few times by their power before flying offscreen.
A funny part is when Midna calls Zelda "Twilight Princess". Ironic, because Midna is the real Twilight Princess.
Similar to in Link's Awakening:
Trill: Pay like you're supposed to next time, cheapskate.
Try running around Castle Town in wolf form. It's funny when all the citizens think you're an enemy monster and they scream and cower before you, but it gets hilarious once all the town's guards start following you around, aiming their spears at you. Too bad they're too afraid to attack, especially since they, too, cower as you pretend to attack them.
While you're at it, do the spin attack in wolf form once all the guards surround you. They run away as fast as they come.
"Hey! You idiot! Don't come over here! AH-CHOO! I finally get my canine allergy under control, and now...Ha...Ha...AH-CHOOOOOO!!"
Just when you think you've finished off Armogohma, the triumphant victory music suddenly stops, and the boss's less-than-impressive true form tries to escape to the sound of a xylophone...just so you can finish it off for real with whatever humiliating tactic you can think of — one of which is standing there dumbfounded for a moment, watching it try and get away, then letting a Bomb Arrow or two loose.
Even better; Link's expression during the reveal is pretty much a Flat "What." without the sound. Priceless.
Try the Dominion Rod; it even grants an extra cutscene showing Armogohma being literally flattened by the statue's hammer. It looks like it got run over by the world's largest steamroller.
Castle Town Malo Mart.
Even better, the text you get when you buy the Magic Armor from the Malo Mart. "You got the Magic Armor! You bought it! You are smart! You bought it at Malo Mart!".
Even the dance they do is hilarious!
The Gorons at Malo's Kakariko Village mart are doing it!
If you look closely, you might notice half the people in Castle Town carrying Malo Mart bags.
One scene during the credits shows the entire town doing the dance in the square.
Using your (strictly prohibited!) lantern in Barnes' shop. He wasn't kidding with those signs!
Barnes' reaction of throwing his hands up in disgust when Renado doesn't introduce him.
Barnes' interactions with King Bulibin; fearfully lowering his mask when KB raises his.
In the desert area outside of Arbiter's Grounds, charging while riding one of those boar-like mounts causes Link to hold on for dear life, with his legs flying behind him.
When you have to revisit the Sacred Grove, Rusl calls over a golden cucco to help you get there. Once you've arrived, morph into a wolf and talk to it. It says "Twinkle twinkle little cucco, I am gold and not for you-oo."
Early in the game, you can hit Malo (the midget of the three kids) with your slingshot and his head will just be knocked back.
One of the first things you can do in the game is go fishing with the rod that Colin made for you. There is a cat looking at fish in the river in Ordon Village. Catch a fish near said cat to gain its attention. Catch a second one and it'll run off with your fish. Link's expression says more than any words ever could.
Fight Ganondorf. Use your fishing rod. Now watch as Ganon stares at the rod, looking at the juicy worm... THEN STRIKE!
In Ordon Village, you can use some falconry skills to knock down a beehive... but for a funny scene, put it off until you talk to Hanch as he's throwing rocks at it. He manages to hit it... unfortunately for him.
Yeto's response if you turn down his offer to race you:
"You no like fun, uh?"
In most Zelda games that have Cuccos, attacking them too much makes them attack you. Not so here: attack a Cuccoo enough (in either form), and the screen will fade to black. When it comes back, you are the chicken, albeit for a short while. (This is not the case for the Golden Cuccoo, or the Oocca.)
During the Snowpeak part of your battle with Zant he grows to a gigantic size and tries to crush you. To make him shrink and become vulnerable, you have to hit him in the foot with your Ball and Chain, leading to an amusing Agony of the Feet moment.
Going back to Ordon village during the day lets you find the Postman hiding in the goat barn, feeding letters to the goats due to the bad handwriting in them.
If you talk to Jaggle a second time near the beginning of the game after he's pointed out the hawk grass to you, he says:
"What's that stuff thinking, growing on a rock like that? I guess I just don't understand grass."
The entire battle with Ook is hilarious not just because of his mannerisms, but because of one thing: his weak spot is his ass. You literally have to kick his ass to defeat him.
Alternatively, he's a monkey, and you have to repeatedly whack him in the behind to beat him. You're "spanking the monkey"!
One of the chickens in Ordon Village blatantly hits on Link in his wolf form. Yes, Link is literally a Chick Magnet.
Beth and Luda's little rivalry over who gets to take care of Colin after he saves Beth from King Bulblin. First they are taking turns wiping his forehead, doing it so often that Renado has to calm them down. Then, after you have returned Death Mountain back to normal and Colin is feeling a little bit better, they are trying to get him to eat and drink something. Luda with her stew and Beth with her specially mixed water (hot spring and sacred spring water combined!), constantly shoving it in his face. Poor fellow...
Any time Link talks to his Fangirls after he won the STAR minigame. The amount of Squee is overwhelming.
EEEEEEK! It's HIM! ♥♥♥ KYAAAAAAAAAAA! *they run off*
The WTF? expression on Link's face after Armogohma (the boss of the Temple of Time) turns into its Clipped Wing Angel form while he's doing his Victory Pose.