The Bomb Bag pickup text. "You found bombs inside! Now you can set them to C and blow stuff up! What a lucky guy!"
In the Spirit Temple, when the miniboss battle with the huge Iron Knuckle is about to begin, a single chord of the miniboss battle music plays, at which point the Iron Knuckle realizes that it doesn't have its gigantic axe, so the music stops, the Iron Knuckle snaps its fingers to summon the axe, and then the battle theme starts over and the sequence properly begins. It's just so out-of-character for the game, like something out of Looney Tunes. See it here.
There's something humorous about young Link playing Epona's Song and getting pushed by Epona.
Darunia gettin' down tonight when you play Saria's Song, complete with psychedelic background!
Darunia: What a hot beat!
If you look during that sequence you can see Link back away very slowly in response, as if Darunia is trying to become a seductive God.
When you finally get the Zora's Sapphire from Ruto, she says you have to marry her now. The following narration is hilarious. Paraphrased, it goes like this: "You got the Zora's Sapphire! Ruto says you have to get married. You're not quite sure what she's talking about, but…"
After the defeat of Phantom Ganon, Ganondorf's last bit of the text:
Ganondorf: What a worthless creation that ghost was! I will banish it to the gap between dimensions!!
Koume and Kotake, the witches collectively known as Twinrova, arguing after they've been defeated.
Koume: I'm only 400 years old!
Kotake: And I'm only 380!
Koume: We're twins! Don't try to lie about your age!
While that particular part takes the cake, the rest of their argument is pretty funny as well, especially considering the fact that they seem to be more concerned with bickering with each other rather than they fact that they're dying.
That's no way to talk to your older sister!
Ingo's groveling when you come back to the ranch after defeating him.
If he stands on the mechanism of the Windmill Hut long enough Link starts to get woozy.
During the Mask-Selling sidequest, when you give the Spooky Mask to the kid in the graveyard, this text box pops up:
You charged him the full price of 30 rupees?! And he didn't even mind paying!
Being ambushed by cuccoos. As irritating as it may be sometimes, there's no denying how absurdly funny it is seeing Link getting his butt absolutely handed to him by a bunch of squawky chickens.
Naming Link Zelda:
"Zelda… Strange, it sounds somehow familiar."
One of the Gorons in Goron City has this gem. It's basically proof that Gorons don't go outside much.
Goron: Oh? We don't get many visitors way up here. Where are you from? The forest? What's a "forest"? It's where a lot of "trees" and "plants" grow? Now I'm even more confused! Nothing grows around here besides the Bomb Flowers… We don't have "seeds" or "nuts" around here either. Even Deku Sticks are very scarce around here!
After you get the Goron mask from the Happy Mask Sales Man, put it on and talk to any Goron and they'll think you're a child Goron. They even tell you to make sure you eat your green rocks.
During the start of the game, Navi (somehow) bumps into one of the holes in the fence. She also says "Hello!" to the girl who teaches Link Z-targeting (L-targeting in the GameCube version and the 3DS remake)
There's a crazy Goron who loves rolling down Death Mountain, leaping into the air when he's about to stop and landing with a BOOOOOOOOOOOOOM!!! Bonus points for funny if you happen to be squishe in the process.
Whenever Mido is acting as an NPC Roadblock, you can engage in some vaudeville-esque slapstick by getting him to waddle back and forth as he mirrors your movements to block you from going forward a la "monkey see, monkey do".