Demoted to Extra: Word Of God says that they would've liked to do more with this character but the network had them give him the shaft because they wanted more focus on Barbara.
Parental Obliviousness: The poor guy can never fully connect with his daughter due to clashing views, and even years into the future, he still doesn't know about her superhero double-life. Justified, as the only time he ever got a good luck at Batgirl was the first time he met her, and he was missing his glasses.
Remember the New Guy: Aside from the Early-Bird Cameo, Gordon's this. Alfred comments that "James Gordon has loomed large over [Bruce's] life." Then at the newly-installed Batsignal, Gordon says to Batman, "Thanks to all of your efforts, Batman, the time is finally right to take our alliance to the next step." Both said despite the fact that prior to "Night and the City," Gordon hadn't appeared in the present day.
Brother Chuck: Aside from a reference in "Artifacts," she's not seen or heard from again after Season 2, though she does appear on occasions in "The Batman Strikes" comic.
Race Lift: She's basically an Asian-American version of Ellen Yindell from The Dark Knight Returns, with her name, her journey from distrusting and hunting Batman to trusting and helping him, and the fact that said mention in "Artifacts" had her replacing Gordon as Commissioner.
Chief Angel Rojas
Asshole Victim: Almost. He was targeted by a newly-transformed into-Clayface Ethan Bennett after how badly he treated Bennett.
Brother Chuck: Disappeared after Season 2 and unlike Yin, nobody missed him or cares.
Expy: He's basically Harvey Bullock with a higher rank and no redeeming qualities.
Jerkass: He doesn't exactly treat a lot of his subordinates with any real respect.
Kick the Dog: His treatment of Ethan Bennett in the Season One finale.
The Other Darrin: Rojas was voiced by Edward James Olmos in his first appearance, then by Jesse Corti in all of his other ones.
Pointy-Haired Boss: Just watch most of the episodes he's in. There's no way in hell this idiot should've gotten as far on the force as he did.
Ungrateful Bastard: Batman saved him and his officers quite a few times and yet he's still an ass towards him.
Jerkass: In his debut towards Batman and Robin. Still, surprising considering that between most incarnations of him and Batman, Supes is the nicer one.
Red Eyes, Take Warning: When he's using his heat vision. Under mind control spores laced with Kryptonite, it's more like Green Eyes Take Warning.
Everyone Calls Him Barkeep: He was only called "Flash" in his appearances and his real name was revealed in a news article about the show.
Hey, It's That Voice!: Charlie Schlatter, who voiced Flash on Superman: The Animated Series voiced Flash here, though according to promo materials the Flash on STAS is the same as on Justice League and hence is Wally West whereas this Flash is Barry Allen.
Personality Powers: Played straight, given his personality is more like Wally West or Bart Allen than the comics' version of Barry Allen.
Combo Platter Powers: In addition to the normal set of flight, shapeshifting, telepathy, super strength and speed, and intangibility/nigh invulnerability, this incarnation also has telekinesis
Last of His Kind: It's generally believed that the Joining killed the rest of the Martians in this continuity.
Weaksauce Weakness: J'onn seems to have a psychological fear of fire. Hence the Joining could point an armed (but not discharged) flamethrower to make him stop.
Follow the Leader: Lampshaded during the first time GA teams up with Bats. Ollie mentions being inspired by Bruce's stuff at the end of the adventure. His appearance in the finale has him using the Arrowplane.
Everyone Calls Him Barkeep: He was never addressed by his real name, but the fact he comments about fighting criminals on two worlds and the comment about the Batcave resembling Thanagar Police Headquarters pretty much confirm he's Katar Hol.
Asshole Victim: As with Rojas, he almost became one. And by the same person, Ethan Bennett/Clayface I no less. And like Rojas, he did deserve Ethan's enmity towards him, basically being the one who more or less made him Clayface.
Berserk Button: Someone getting in her way, more so if you're intervening in her heists. Ragdoll will vouch for that. Also - don't threaten any feline creature. She doesn't like that.
Whip It Good: Just wouldn't feel right without it.
The Riddler
Batman Gambit: He has set fake bombs all over the city that can only be deactivated by solving various puzzles. This is actually a diversion so that he can break into the City Hall database undisturbed and steal important information. He actually got away with it!!! (Until he had a Villainous Breakdown)
She Is All Grown Up: In her last appearance in The Batman Strikes, her body is drawn in a more adult way, showing that's she finally growing into the full-fledged seductress she's known as in other continuities.
Be Careful What You Wish For: He wanted all the knowledge of the universe for helping the Joining. He got it and became catatonic because they telepathically broadcasted it into his mind.
Chekhov's Gunman: Makes his first, brief appearance in "Meltdown" and goes on to become much more important that the scene lets on.
Multiple Choice Past: We don't know whether he's a military genetic experiment gone awry, he deals with the wrong kind of voodoo magic in the swamps, or if he's simply a circus freak.
If the tie-in comic, The Batman Strikes counts as All In The Manual, then according to issue 25, he was both a military genetic experiment subject before escaping, then was part of a circus freakshow before escaping that and ultimately coming to Gotham, though it's still unknown if he was born like that as in the comics or if being part an experiment is the reason for his appearance.
Enemy Mine: He tries to help Batman take down the Joker when he resurfaces, but Batman won't let him out of concern for his mental health. When the second Clayface appears, Batman and Robin willingly let him help them take the new guy down.
Heel Face Revolving Door: Starts out on the Face side, goes into the Heel side briefly, makes another attempt on the Face side briefly, slips back into the Heel side, then in Season 4 ended up back of the Face side and stays there.
How Do I Shot Web?: At first: it doesn't take long for him to get dangerously good with his powers.
That Man Is Dead: He tells Batman and Ellen to say goodbye to Ethan Bennet after his first shot at returning to a normal life. Subverted when he manages a Heel Face Turn later anyway.
Basil Karlo/Clayface II
Attention Whore: Not only doesn't he even try to hide from security cameras, he'll look into them and boast about what he's going to do. He also went on a news program and tried to tell a bogus sob story. In fact, aside from a brief instant when he went What Have I Done after attacking some people for rejecting him for an acting job, he embraces it after realizing he's famous because of it now and got angry when Batman was mentioned in the aforementioned news program.
Bad Bad Acting: He wasn't a good actor before he became Clayface and he still sucks at it when he gets his power.
Dark and Troubled Past: Subverted as he doesn't really seem to have one and parodied it as he tried to tell a story where he and his sister had to fend for themselves, but the reporter he tells it to clearly wasn't buying it.
Berserk Button: Not only was she upset that she got fired and her show canceled and a new show takes over her time slot, but the psychiatrist of that show plans to talk about how being fired caused Harley to have a "mental breakdown".
Curb-Stomp Battle: Does this to Batman, though for different reasons than in Knightfall. Mostly the fact that using Venom turns Bane into a Hulk-like figure in this incarnation and that his debut was in the second episode of the whole series meant he was going up against a Batman still getting used to fighting supervillains and whose only prior experience at that point was the Joker.
The Other Darrin: He was voiced by Joaquim de Almeida for his debut in "Traction," then by Ron Perlman for his cameo in "Team Penguin," then his grunts by Clancy Brown in "The Batman/Superman Story."
Bad Boss: Never let yourself get delayed or question his plans if you value your life as two of his Number Ones learned the hard way. He'll also assign a random mook to take over as Number One.
Shout Out: Oddly, despite being, well, Black Mask, his methods in his debut episode resembled the Joker slightly more, when somebody's not useful anymore, he just says "You! You're the new number 1!".
Clancy Brown: Again and appropriately enough, one of the Bat-villains he hires during his episode was Brown's role of Mr. Freeze. Sadly, Freeze only grunted, so no real use of Talking to Himself.
Not to mention that Luthor and Freeze didn't share scenes anyway.
Fantastic Racism: Similar to other recent incarnations of Luthor, this version has a hatred of aliens.
Kneel Before Zod: Forces a mind-controlled Superman to bow to him.
Mirror Master
Composite Character: Of Both Mirror Masters. He has Sam’s genius intellect and charisma as well as Evan’s “I can do anything I think of with mirrors” ability.
Blessed with Suck: Arguably, the clones he creates become progressively more and more sentient, and every multiplication equals an even more untrustworthy clone, this ability only comes in handy a few times, a long fight isn't exactly smart.