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 distracted by Panic drinking some Hercu-lade.)
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!
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.
Another from the series, we have this masterful Gilligan Cut from "Tapestry of Fate":
Icarus: Oh relax! The worst [the Fates] could say is "no"!
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)