Any time Link can attack Cuccos...only to have an endless swarm of killer Cuccoos chase after him in revenge.
Late in "The Missing Link," Ganon states that Zelda is able to see Link's non-corporeal form due to The Power of Love. Both Link and Zelda are in earshot of this. Zelda profusely denies this to Link...
Link: Yes you do!! Yes you do!! *sings* That's why you can seeeee meeeee!!!! *stands up on a ledge to proclaim the glorious news to the rest of Level-9*
The entirety of "The Moblins Are Revolting," where Ganon's army is so incompetent they defeat themselves.
Even the beginning, where they come close to stealing the Triforce of Wisdom as Link reads a comic book, and they defeat themselves easily.
Link: Boy, I'm good.
Link telling the Moblin leader that their plan is the stupidest plan Ganon ever conceived, only to be told that the monsters thought it up themselves.
The Moblin leader tells another Moblin to be careful with the magic staff and to not drop it. When the other Moblin asks him to repeat the last part of the order, he yells "Drop it, stupid!" causing the other Moblin to do just that. The Moblin leader, hearing the staff break, does a Face Palm and muses that now he knows how Ganon feels.
Ganon's reaction when he is pushed into the Bottomless Pit while trapped inside a bubble.
In "That Sinking Feeling," Zelda is overjoyed at a picnic Link has set up and glomps him. She's just about to kiss him when Ganon attacks and ruins the mood.
Zelda: It's an underworld entrance. We're being attacked! Link: They couldn't have waited ten seconds?
In "That Sinking Feeling," Ganon's reaction when he finds the Triforce of Wisdom is missing is to throw a tantrum and yell "I'M VERY UPSET!"
King Harkinan and Spryte keep having to hide from him in increasingly funny places.
In Cold Spells, Ganon sends a Gohma to eat Link and Zelda. Of course, Gohma attempts to grab them from the side of the container. Ganon's response is this:
Ganon: No, Gohma, no! Reach down from the top!
Ganon falling into his own trap in "He Also Serves" ends up as this due to the sheer amount of Epic Fail involved. After spending the entire story shapeshifting into various characters to try and get Link to leave North Palace, Link realizes that it's Ganon and has the gates sealed to keep him trapped inside. Ganon, in a desperate ploy to escape, turns himself into Link and rescinds the order to the watchman. Only he forgets to change forms again after leaving and his minions are none the wiser when they spring the trap.