In the episode "The Eldritch Mist", Shadow Weaver and Castaspella have a brief duel of magic. Castaspella counters each of Shadow Weaver's spells and renders them colorful and harmless. The duel culminates with Shadow Weaver setting a monster on Casta, but it's transformed into a big, smiling teddy bear, which goes after Shadow Weaver and gives her a hug. Shadow Weaver is absolutely terrified.
In the episode "The Stone in the Sword", Adora (temporarily unable to become She-Ra) has to climb up Skydancer Mountain, while Kowl flies up beside her. After she almost loses her footing, Kowl delivers one of his best lines ever: "If you should fall, I'll keep you company all the way down." The dirty look Adora shoots him just makes it funnier.
Hordak is using a new battle cruiser on She-Ra and He-Man when it suddenly loses power. Turning, he finds the culprit:
Hordak: Skeletor! You lousy two-faced turncoat traitor!
The two then go at it in a big battle and don't realize until too late that they've basically destroyed the star cruiser they were fighting over. He-Man and She-Ra, meanwhile, are just sitting back and enjoying the show.
"Loo-Kee Lends a Hand" has probably the greatest out-of-context Ho Yay moment ever:
Skeletor: With this crystal I can create a portal right into Prince Adam's bedroom!
The entire episode of "Flowers for Hordak" is one hilarious moment after another. Once we see Perfuma dancing with a Hordesman it's pretty much non-stop hilarity.
Watching Perfuma create flowers around his kingdom and lead his robot soldiers in a conga line, Hordak transforms his head into a hammer to slam against a wall. "No...no...no...no..."
She-Ra arrives, expecting to have to rescue Perfuma only to find Hordak literally begging her to take the woman away. Realizing she's got him over a barrel, She-Ra not only gets Hordak to lift a spell of darkness on the forest but also give up a priceless ruby and three months worth of supplies. Hordak considers it a small price to pay to finally get his kingdom back in "order."
In "Anchors Aloft, Part 2," Sea Hawk is forced to choose between going after gold thrown into the ocean or pursuing a villain to save She-Ra. He does the latter, which Adora later compliments as noble. It's at that moment that Hawk's first-mate surfaces from the water and reports that he found the gold... right where Hawk said he saw it fall.