Executive Meddling: According to the Word Of God, Batwoman had her civillian identity changed from Kathy Kane to Katrina Moldoff after DC Comics executives voiced concerns about how the negative portrayal on the show might impact sales of the current Batwoman comic book series, which stars the similarly-named "Kate Kane".
John DiMaggio was also Kimahri and Wakka from Final Fantasy X, which makes it hilarious whenever he teams up with Green Arrow (as stated below, James Arnold Taylor played Tidus). This version of Aquaman even has a water sword, like Wakka's brother's sword Brotherhood.
The reason Tom Kenny plays Plas is because he had the role in a pilot for a Plastic Man cartoon that was never picked up. The creators liked how he did in the pilot, and gave him the role just so he could play him again.
Jeff Bennett, voice of the BTAS version of The Creeper, as the Red Hood and the Joker.
And Batman's singing voice.
Try watching a Joker episode back-to-back with The Penguins of Madagascar. It's hard to unhear the nuances between Kowalski and Joker's voices.
Corey Burton voices the android Red Tornado using the same voice he used for Brainiac. (Which makes it hilarious when he deadpans "I feel a pleasant tingling sensation!" and creepy when his Evil Counterpart starts talking about its hatred of living things.)
She's also Billy Batson, which is a bit more typical of her.
Meanwhile Grey DeLisle did the voice of Black Canary, using that cool Vamp voice she does so well. Except this time her character isn't evil. She also voiced Black Canary in the DC Showcase: Green Arrow short film after playing the character on the Brave and the Bold.
Kevin Conroy is the Batman of Zur-En-Arrh and the Phantom Stranger. Joining Conroy in "Chill of the Night!", Mark Hamill is the Spectre, Adam West as Thomas Wayne, Julie Newmar as Martha Wayne, Jennifer Hale as Poison Ivy and reprising the role of Zatanna from Justice League. Additionally, Two-Face is Lew Moxon and himself and Warhawk killed Batman's parents.
Hal Jordon is Loren Lester aka DCAU's Robin and later Nightwing. It's more noticeable in the game. Where he's a jump in hero.
The Japanese dub, besides having Tessho Genda reprise his role as Batman again, also had a really top-star voice cast of many well know voices from anime:
Name's the Same: Shark of the Terrible Trio shares a name with Shark, an actual tiger shark mutated into a humanoid form who had a cameo in "Night of the Huntress!" And neither of them are to be confused with Tiger Shark, of course.
One of Us: Oh so many examples of the fact that the staff is as big of nerds as us, in particular "Mitefall!".
Playing Against Type: Diedrich Bader as Batman. That's right: a guy known for playing The Ditz is the lead. To a lesser extent Will Friedle as the Blue Beetle, who is known for playing characters similar to Bader's.
Screwed by the Network: If giving the final season 13 episodes when the first two had 26 wasn't enough Cartoon Network also managed to anger the fans more by airing the season's episodes with weeks, sometimes a month, between new episodes and without much promotion.
What Could Have Been: In "Game Over for Owlman," according to Word Of God, it was considered including Terry McGinnis as one of the alternate Batmen. They relented, however, due to it being so early in the series' run - preferring to stand on their own before going so meta.
A fairly minor example, but according to the cover to the comic's first issue Katana was slated to have a wildly different design — one more evocative of mainstream DC Katana, but, like, mostly purple. And pigtails.
The identity of the Robin in the teaser is unknown, since the last time he appeared he switched over to Nightwing. It may have been meant as a flashback, or it's a new Robin.
In the Episode "Bat-Mite Presents: Batman's Strangest Cases!"
It features Scooby and Batman dual-punching the Joker after Bat-Mite uses his powers to allow violence.
Funny enough, when Bat-Mite notes that someone mispainted Batman's collar, he doesn't seem to notice the fact that the Bat-symbol is inverted.
In "The Vile And The Villainous!":
Joker and the Weeper teamed up once before, in the Justice League of America comic book issue #136.
Joker and The Weeper actually succeed in destroying Batman's crime-detecting device (but get arrested anyway).