In the first Lil' Bat short, Pablo/Lil' Bat has woken up early in the morning, and proceeds to pour himself a bowl of cereal. Cue the stream of milk going up, and the camera perspective flipping up to reveal he's standing upside-down in his cave.
In Mysterious Egg, the team are overpowered by the monster of the week and prepare themselves for the worst...
Ricky: Do you think pancakes can talk in heaven?
Eaglebones: Ricky, we've had this discussion; pancakes can't talk.
In one of the band cartoons, MC Bat Commander stands proudly on the moon. Breathing normally without an apparatus of any kind. While the rest of the band gets attacked by SPACE BEES in the background.
The recap of "The Haunted Battle Tram!" right before "Cowboy Android!" is just a minute or so of non-stop screaming. Ditto the one for "Night Of The Cactus" that airs before "CobraMan!", because it's a montage of Ronmark getting slapped in the face. Repeatedly.
When about to face the android sheriff, the band (sans MC Bat Commander) line up wearing hubcaps (nicked from the abandoned car park) nearby to use as shields against the android's laser gun. Except for Crash Mclarson, who has an entire suit of armor built of the things. Including one on his groin. Naturally, the sheriff shoots him in the one place he didn't protect...
Sheriff: [shoots Crash in the foot]
Crash: MY SHOE!
"Cobraman!" gives lots of hilarity for the sheer fact that our main villain's voice and mask scream Strong Bad.
"The Floating Eyeball of Death!" gives us this:
Jimmy: Once upon a time, there was giant floating eyeball that flew across the land...
Crash: I like this story!
Jimmy: In search of human souls to devour!
Crash: I don't like this story!
EEEEEEEEEEEEEEAAAAGLECLAAAAAAAAAAAAAAAAAAAAAW!!! hamming it up.
The ending of the first episode, where the MC Bat Commander says it best.
Bat Commander: Burger Rain!!!
One from the development: On the Mega64 podcast, Rocco told a story about being on set and ranting about how Italian restaurant chain Buca Di Beppo is terrible, when all of a sudden, MC Bat Commander pops up out of nowhere, in full costume, and chimes in, "Well, they have good desserts..."
In "Eagle Claw," when Eaglebones dramatically reveals Eagle Claw as "My brother...!," and once he's done, the Aquabats just stand there, continuing to stare at him, and Ricky busily takes a sip from his drink.
After the Sudden Downer Ending of Season 1, Season 2 opens with the Aquabats waking up with very long beards.
The MC Bat Commander gives his origin. When the topic of his teammates' powers comes up (and subsequently asking what type of powers the Bat Commander himself got...which was none), the Commander can only gasp out, "Dude, mind your own business!"