Actor Allusion: In Batman Beyond, Will Friedle played Terry McGinnis, a high-school student who recently became a Power Armor-wearing hero and had to learn the ropes from Batman. In this series, Friedle plays Jaime Reyes, a high-school student who recently—you get the idea.
Also, in Boy Meets World and Kim Possible Jason Marsden played Will Friedle's best friends: Jason and Felix, respectively. Here he plays Blue Beetle's best friend, Paco. Also reprising his role as the Normal Best Friend of a teenage superhero from Static Shock.
Executive Meddling: According to the Word of God, Batwoman had her civilian 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". She was also not referred to by her codename in the episode, except for a throwaway line about a "Bat-lady".
Irony as She Is Cast: Given a nod in the episode "The Mask of Matches Malone!", which features a scene where Catwoman jokingly suggests that Black Canary being gagged by the bad guys is a good thing because she supposedly has a terrible singing voice when in real life, Black Canary's voice actress, Grey DeLisle, is a Grammy-winning professional singer. Subverted in practice — as heard in both "Mayhem of the Music Meister" and this very episode, Canary's singing voice works just fine (no problems from abusing her vocal cords with that "canary cry" of hers, it seems) — but then that's Catwoman for you.
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.
Non-Singing Voice: In "Mayhem of the Music Meister!", Batman's "singing" voice belongs to Jeff Bennett rather than Diedrich Bader. Also lampshaded by Batman:
Batman: I'm actually more of a baritone. I was only able to match you using this Bat autotuning device."
One of Us: Oh so many examples of the fact that the staff is as big of nerds as us, in particular "Mitefall!".
The Other Darrin: In Katana's debut appearance, her few lines were voiced by Vyvam Pham. While she was silent in the teaser for "Duel of the Double Crossers!", she was voiced by Kim Mai Guest in "Inside the Outsiders!"
The weird thing is that her first appearance features a normal American accent, while she gets a Japanese one in her second.
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.
Recursive Adaptation: "Night of the Batmen!" is based on an issue of the series' own tie in comic. Let that sink in.
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.
"The Masks of Matches Malone!" episode has not aired in the US, after much attention was given online to the innuendo in the Birds of Prey song. (However, it can be found as a bonus episode in the Season 3 DVD set.)
What's more episodes are broadcast with no regularity whatsoever, there can be months between two consecutive new episodes.
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.