Accidental Innuendo: In Laundry Day, the 'Bats are repeatedly whipped by a monster. Ricky groans that he's never felt so dirty before in his life. He's of course actually referring to the the dirty clothing the monster is made from.
During their fight in Christmas With The Aquabats, the Krampus demands Santa punish him for being naughty.
Family-Unfriendly Aesop: Christmas With The Aquabats has the cast decide that parents should spank their kids more often instead of rewarding them on Christmas with gifts even if they've been bad. Then subverted when the characters seem perfectly fine rewarding everyone, good or bad, so long as the Krampus isn't watching.
Fanfic Fuel: The show runs on Rule of Fun, but occasionally sprinkles little details and bits of continuity that could be worked with, such as Weird Al playing both the President and Super Magic Power Man who dies, and the purposely contradicting back story segments in Season 2.
Fanservice: Of the non-sexual sort. Mythology Gags abound, whether the basis for an episode (Showtime, Shark Fighter, Cobra Man) or more subtle and in the background (The band's purple uniforms being used as camouflage, Crash's narration quoting lyrics from Pizza Day in The Thingy.)
First Installment Wins: Thanks to a halved second season and an even smaller third (Three Episodes!?), the show sadly hasn't gotten as much attention after the season one final.
Fridge Horror: Episode 9 ends with Pilgrim Boy being asked to transform into fireworks, which he does. Then said fireworks go off.
A good chunk of people at the Aquabats! Super Show panel at Comic-Con 2012 were only there because Gerard was moderating it. Made funny during the panel with a load of teenage girls in the front cheering his introduction...with some Aquabats! fans further back asking each other who the guy was.
Special mention to Space Monster M. He's a hammy, giant, floating, albino head with a large M on his forehead... and he's terrifying!
Newer Than They Think: Fans of the show may check out the bands' earlier stuff might be surprised at how new Ricky and Eaglebones are to the cast, as well as the band not having set powers and the complete absence of the Battletram.
They Wasted a Perfectly Good Plot: In Showtime!, real life former Aquabats! Catboy and Chainsaw appear as rival superheroes. Instead of arguing, they decide to team up! And then Super Magic Power Man and Lanolin Lady show up, so Catboy and Chainsaw just leave.