Baby Hercules chewing on a lightning bolt and tying Pain and Panic in a knot.
Herc's reaction to the Zeus statue coming to life — granted, that's probably how anynormal person would react if a giant statue came to life and started talking to them.
Almost all of the scenes with Hades (played by James Woods, who apparently improvised many of his lines). The numerous mythical/historical in-jokes were also great.
An example of Hades's wellspring of comedy:
Titans: DESTROY ZEUS!!!
Hades: Uhh, guys? Olympus would be that way.
Titans: (look at Olympus like "WTF...?", then turn around and walk towards it) ...DESTROY ZEUS!!!
Nearly every time Hades goes off on one of his rants.
Hades: I am about to rearrange the cosmos, and the one SCHLEMIEL who can louse it up IS WALTZING AROUND IN THE WOODS!
Upon finding that Pain is wearing Air-Hercs:
Pain: Um, I don't know. I thought they looked kinda dashing.
Hades(getting flamier with each phrase): I've got twenty four hours to get rid of this bozo, or the entire scheme that I've been setting up for eighteen years goes up in smoke, and you...are wearing...HIS MERCHANDIIIISE?!
(Hades almost flames Pain before getting distracted by Panic drinking some Hercu-lade.)
Hades: I KNOW!!!!You know. I got it, I got the concept.
The last words in the movie are in The Stinger, and guess who says them? You got it:
Hades: What díya say? Itís happy ending time! Everybodyís got a little taste of somethiní but me. I got nothiní. Iímó Iím here with nothiní. Anybody listeniní? Itís like Iímó What am I, an echo or something? Hello? Hello? Am I talking to, what, hyperspace? Hello, itís me. Nobody listens.
The brave, heroic title character that just awesomely KO'd a centaur that was more than quadruple his size (which is really saying something) being reduced to a stuttering, AdorkableShrinking Violet when he first meets Meg.
Just the centaur getting KO'd with his horseshoes flying after him. It's straight out of classic toons! No Trailer Joke Decay here!
Phil making fun of the idea that Zeus is Hercules's father.
Phil: Zeus?! The big guy - he's your daddy?! Mr Lightening Bolts? 'Read me a book, would you, da-da?' Hahahaaa, Zeus! 'Once upon a time!'...
Later, during Phil's song, he tells Herc that even if he is Zeus' son, he won't train him. Zeus convinces him to in the most epic way possible.
Phil: My answer is, TWO WORDS: (gets hit by lightning) okay...
When Hercules starts fighting the Titans, the Lava Titan spews some lava on Hades in an attempt to get Herc.
Hades: No, not me! Him! (Ice Titan goes after Herc, who flies by Hades) Follow the fingers, him! (Gets frozen) The yutz...with the horse!
"Two words: I. Am. Retired." Bonus points since the phrase in Greek is actually two words long. Especially because Herc looks baffled trying to sort out how that counts as two words.
Herc defeating a one of the Stymphalian birds...by locking her in a giant birdcage. Her disgruntled "are you kidding me?" look is what really sells it.
Megara backs into a Cupid (or would that be Eros?) statue. Specifically she pokes herself with his "love arrow." She notices this, and shows an expression of "does that mean what I think it means?" Look at it!◊
Meg's introduction clues us into how snarky she is with several lines.
Hercules: Are you alright miss...
Meg: Megara. My friends call me "Meg", or at least they would if I had any friends. So, did they give you a name with all those rippling pectorals?
(Herc babbles incoherently)
Meg: Are you always this articulate?
Hercules: Hercules. My names Hercules.
Meg: Hercules? I think I prefer "Wonderboy".
Hercules: So, how did you get mixed up with the—
Meg: Pinhead with hooves? You know how men are. They think "no" means "yes" and "get lost" means "take me I'm yours"! (does a mock swooning pose to Herc)
Thalia the Muse is full of them, especially during the "I Won't Say I'm In Love" sequence, where she waves the flower at Meg and is ignored, she ends up dangling from the 'ceiling' the others have raised up, she's held up by the others during the line "you (got) (got) got it bad," and how her head isn't attached to the rest of her bust, which results in her lounging on the column.
The Swedish dub of Zero to Hero mentions MTVby name.
In the series, Bob the disembodied voice narrator is informed by the Muses that everyone gets a day off to celebrate Titan Smiting Day, including him. Later during a local festival, we see four celebratory hats floating through the air which apparently belong to Bob, his wife and two kids, who thank him for taking them to the festival.
Also from the series, specifically "Hercules and the Big Show", Zeus gives Herc a lightning bolt with this comment, in reference to Hades:
I think it's time my son tried his hand at the family business — smiting the wicked.