Creator Backlash: Freakazoid's "low bridge" chant in Dance of Doom was hastily adlibbed by actor/writer Paul Rugg and was only meant as a place-holder until he and the rest of the crew could think of something better. When it ended up being in the finished episode, he was not pleased, to say the least.
The show was never popular amongst WB executives, who didn't like how the ratings skewed much higher than they intended. It ultimately ended after two seasons when a regime change in studio management decided to clear just about everything out of their Saturday Morning Cartoon lineup. To justify this, they instituted an ad gimmick called "Big Kids Come First", where all the adult-skewing cartoons were aired earlier than the ones skewing for younger kids, making sure that nobody watched anything and ensuring that ratings dropped low enough to justify a massive overhaul.
Throw It In: See that Moment Of Awesome from the first episode? Originally Freakazoid was just supposed to say "No!", but Paul Rugg improvised the rant.
According to the DVD commentary, it apparently went on for over 10 minutes, becoming increasingly disjointed and profane. It got cut off before the swearing started.
Rugg actually improvised a lot of his lines in the show in general, including the part in the first episode where he sings off-key. You can hear him trying hard not to laugh at the ridiculousness of his own lines.
What Could Have Been: The original idea was for the series to be a fairly straightforward superhero show with comedic overtones (The Joker as a good guy) with Bruce Timm in charge. Spielberg, however, asked for a full-blown comedy. Timm bowed out, as he honestly thought he wouldn't do a full-blown comedy concept justice. This is perhaps a textbook example of Executive Meddlingimproving a show. (The New Batman Adventures episode "Beware The Creeper" is a glimpse of how Timm and Dini would have done Freakazoid!)
The series always skewed towards an older audience and there was serious consideration towards just putting it in prime-time (as was done with Pinky and the Brain). This is part of the reason why the second season largely had half-hour episodes instead of Three Shorts.