The early scene in Wind Waker where the pirates reveal exactly how they plan to get Link into the Forbidden Fortress may well be one of the funniest things in the entire Zelda universe, bar none. Link needs to get inside, but the place is swarming with patrol boats. So what do they do? Stick Link in a barrel, put him on a catapult, and wish him "Bon voyage!" Seriously. The look(s) on Link's face during the countdown itself are priceless — but the pure slapstick of him splatting into the wall on the other side once they launch him is pretty good too. (The only thing that's not funny is the stealth-due-to-lost-sword that follows.)
That scene is closely rivaled by the cutscene after Link places all three pearls of the goddesses. After placing the last pearl, the statue begins radiating beams of light. Link naturally yells and dives for cover moments before the statue... does nothing. Cut to Link's bewildered reaction, after which he goes back to inspect the sta-KABOOM! "WAAAAAAaaaaaaaa..." *ding*
As the Tower of the Gods rises out of the sky, Link crashes right into it- splat!- and falls into the water. The King of Red Lions just talks at him like nothing's wrong and tells him to get going. Honestly, it's like they decided on the graphics style just for the slapstick and ending.
When you get 30 points in Beedle's ship shop, you get the Complimentary ID. Show it to Beedle, and he... compliments you.
Chuggaconroy had a bit of a breakdown when it happened to him. (It starts around 8:45 or so)
In the Earth Temple (and before the Dragon Roost dungeon), throw Medli directly at a wall. Slapsticky, yes, but effective, especially when you do it as explicit punishment for her awkward jumping controls.
If you do it at Dragon Roost Island, before throwing her on the cliff so she can go on ahead, she'll mutter gibberish, like the following:
Medli: Huh? Whuh? Link? Since when did you become triplets? No, I'm five... I mean, file... FINE! C'mon! Don't hold back! Use the wimp... er...WIND and really toss me!
Medli: My, what beautiful stars! Twinkle-twinkle... Where were we? Oh, yeah! Once...once more! With the wind! Toss away, please!
Heck, throwing Medli or Makar into a wall is pretty funny, whether on purpose or on accident (maybe even more so if you discover you can do it by accident). Mean, yes, but still pretty funny, since you can do it over and over again without actually hurting them (as they have no Life Meter).
On Windfall Island, you can play a Battleship-like game in a shop for a Piece of Heart, complete with sound effects being provided by the very bored man who runs the place. The "splooooosh!" sound he makes every time you strike an empty square is priceless, not to mention his face if you say you didn't understand his explanation.
His attempt to portray the children you saved is also hilarious, but pales before his antics at the cannon minigame on another island. Win there and he plays the role of a flirtatious young woman... which happens to be Tetra.
Despite the intimidating-looking Darknuts, the fierceness is lost when you remove their helmets and hit their heads with a boomerang, making them see stars.
The meowing sounds Link makes to throw a robber he's following in Windfall Island off his trail.
This troper once made Link make this noise while the robber was looking at him and he was in plain sight. The kicker? She looked like she would've bought it, being about to turn around. It failed, of course, but it was uproarious.
When Link is out in the water too long, the noises he makes are hysterical.
The "BASH" sound when you deal the finishing blow seems surprisingly violent for such a vivid world, especially when a Stalfos is defeated since you get to hear an anguished "Arrrrgh!" along with it.
Especially that honking sound a Miniblin makes when you squash it with the Skull Hammer. Given how much annoyance and Nightmare Fuel those things provide, that can also slip into Most Wonderful Sound territory.
The Re-Deads have amusing deaths. Instead of just melting away like in OoT, they randomly explode after ten, fifteen seconds.
Link's meeting with the Fairy Queen. She tells him that he's just her type. Link seems really happy about this, until the boat gives him a look.
What happens when you attack a Moblin in the rear (made all the more amusing due to the fact that it's quite a beefy-looking enemy): it hops about clutching its behind, with tears streaming from its eyes.
The first meeting with the Deku Tree. He sees how Link is dressed and starts speaking ancient Hylian, which only he and the other spirits can even understand nowadays. After a few lines of unintelligible dialogue, it cuts to Link, slackjawed and having no idea what he's supposed to say.
Break apart a Stalfos and pick up its mace, then wait for it to reform and get close to it. It will look at its empty hands, pull off one of its arms, and use it as a nunchuck to hit you!
The real funny bit about this is the SOUND they make while coming at you like that.
Oh, but you can go so much further! Target it and throw your boomerang at it—its head'll spin on its socket, and it'll have to stop and knock it back into place.
It's also possible to cut them in half at the waist with a Spin Attack or a sideways hit with the Skull Hammer. If you manage to do it, the legs will keep attacking Link by kicking at him while its upper body starts running away on its hands.
Related, drop a bomb down into an area with Moblins and they'll attack it, with predictable results. Drop another and they'll run away panicking!
Or lure them close together so that they accidentally hit one another trying to attack you. After a couple of hits they'll lose their temper and hit their fellows in revenge!
The New Game+ bonus of not wearing the traditional green outfit is introduced in the most hilarious of fashions. Link's grandmother hands him nothing and he has this miserable look on his face. She asks him what's wrong; it's apparently made of a special material that only the honest can see - which becomes a running gag as you get to see which characters in the game are honest. The Item Get text is confused by trying to say "Link got... nothing? wait..." and Link pretends to put the clothing over his pajamas and then you realise throughout the whole game Link was wearing his pajamas underneath the green outfit!
It is especially humorous to discover that Link's sweet and innocent sister Aryll can't see it, but the pirate leader Tetra can.
Not only that, but guess who can also see it. GANONDORF.
The funniness is pumped up when you use the Magic Shield in the second quest: It forms an outline of the Hero's Clothes (hat and all). Developer's oversight or Fridge Brilliance?
Link's face when a Great Fairy doubles his magic meter.
Go to Ice Ring Isle and stand on the ice. Start running in one direction, then immediately start running in the opposite direction. Link will slip and fall on his face.
The HD remake introduces selfies. The internet had a field day with this.
Normally, giving Carlov a Pictograph of a correct subject will give him the usual inspiration, and that you'd have to wait until the next day for the figurine to be completed. But snap a picture of him and he'll say it's beautiful.
The sheer number of uses for the All-Purpose Bait. Just try using it on Snake!Puppet Ganon.