These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Character Alignment: Played up in "The Fate of Equinox!", where Batman and Dr. Fate are portrayed as Chaotic Good and Lawful Good respectively. They also deal with the True Neutral Equinox. Much squabbling about order, chaos, and the powers that be ensues. When Batman points out that Equinox is truly Neutral Evil, it causes him to have a Villainous Breakdown.
Complete Monster: General Zhal. He forces the Doom Patrol to sacrifice one innocent person in order to spare millions of people in Paris, causing the Doom Patrol to split up. They are brought back again, this time with the General threatening to destroy an island fishing village if the Patrol don't take the places of its people. This time, they DO make the sacrifice—and Zahl kills them.
The Faceless Hunter. His entire reason for joining Starro is because he hated his home-world's peaceful lifestyle and enjoys Hunting the Most Dangerous Game. But what pushes him into this is after Starro is killed by Earth's heroes, he kidnaps B'wana Beast and uses him to make something worse than Starro with every intention of doing so because he likes causing planet wide destruction and death.
The Psycho Pirate. The guy traps people in their worse nightmares and feeds off the rage of children. He's so evil, Batman get's openly furious at him!
Batman being crushed with a giant hammer and his soul drifting to heaven replete with harp, angel wings, and scowl, corny; him being melted in a vat of acid to the bone horrifying, everything afterwards is just plain funny.
Crowning Moment of Heartwarming: admit it, the ending scene to mitefall, especially Batman's breaking the fourth wall speech to the audience brought a tear to your eye.
Ear Worm: Pick any song from "Mayhem of the Music Meister!"...
The Muuusic Meisterr... Is the man that the world shall obeeey..! Drives us bats! Drives us bats! He really drives us bats! Bats! Bats! He drives us baaaaaats!
Also, the one and only Birds of Prey.
"Where's The Fun In That?" from "Emperor Joker!".
"Gray and blu-uuuuuue, gray and bluuuuuue..."
Ensemble Darkhorse: Aquaman, made more awesome, given that DC Comics originally intended Blue Beetle III to be the breakout guest-star of the series. By ratcheting up his Superfriends uselessness into a hammy parody of the character, AQUAMAN's become a hilarious form of Mythology Gag. And considering that he turns out quite competent, he sort of delves into unexpected Rule of Funny-endorsed awesomeness.
The Music Meister. That fact that he's voiced —and sung— by Neil Patrick Harris probably has something to do with it.
Blue Beetle III was also a bit of a Darkhorse - this series is responsible for turning a lot of people on to Jaime's comics.
Evil Is Sexy: Catwoman. Well, as Batman himself says, she's not exactly "evil" persay, like his other villains, but he does seem to like her more when she behaves meaner. Like this dialogue from "The Knights of Tomorrow!";
Bruce Wayne: I forgot how cute you are when you're threatening
Morgan La Fey
Family Unfriendly Aesop: Intentionally or not, the Atom episode had the hero win by violence rather than his wits.
Foe Yay: Taken beyond subtext. Batman lets Catwoman escape, Catwoman gives Bats her number.
Heatwave, Weather Wizard and Captain Cold all have this for Barry Allen when the world thinks he's dead. They interrupt their own robbery to complain about how boring and unimaginative an opponent Batman is next to him, and how "Geezer Flash" and "Baby Flash" just aren't the same. They're quick to deny it when Batman accuses them of missing him, but their delighted reactions when he returns say otherwise.
Sorceror Felix Faust helps Batman undo Batwoman's spell that switched their bodies, all the while thinking that 'Batwoman' was the same woman she'd always been, oblivious to the fact that the original spell had done its job. When he's talking about how he'll miss her after the body-switch was successful and Batwoman's off to prison, Batman asks him if he realizes that it was him in Batwoman's body. He smirks and replies:
Jonah Hex and Lashina are positively dripping with Foe Yay throughout "Duel of the Double Crossers!" It even ends with the two of them riding off together.
Bordering on Ho Yay when Bats teams up with the Joker.
Joker when Bats brings him to the Batcave and he sees the mementos inside: "An entire wing for moi? I knew you cared!"
Bat-mite lampshades Batman's relationship with Joker in "Emperor Joker". Then it is deconstructed when we see how horrible it is to be on the receiving end of Joker's attacks; even Bat-mite realizes it since he's helpless and chased by his own "Mini-Joker".
Genius Bonus: In "Mayhem of the Music Master," the titular villain at one point flees from Batman along five telephone wires arranged like a musical notation staff... and his quarter-note-shaped vehicle jumps from line to line to follow Neil Patrick Harris' singing.
Harsher in Hindsight: In "Dawn of the Dead Man!", Batman is trapped in a limbo between life and death, acting as a ghost. He sees the gateway to the afterlife, with his parents urging him to join them. This is a little unsettling given that the episode premiered two days after the release of Final Crisis #6, which ends with Batman's death. Or as revealed at the end of the last issue, what looked like it at first glance.
And this episode shows the start of Deadman's friendship with Batman. In Justice League, we saw such a relationship come to an end. Deadman was forced to possess Batman to save the heroes from Devil Ray, killing him, but when it's over Batman realises he did it by using a gun. Bats does not look happy about it.
In "The Knights of Tomorrow", Old Joker is given six months to live due to the chemicals he's used over the years. Now, take a look at Joker in Arkham City...
Hilarious in Hindsight: The very first episode has Blue Beetle arguing that Batman would always beat Superman in a fight because "Batman always has kryptonite". The third season kicks off with Batman actually fighting Superman...and he doesn't have kryptonite. And gets flattened.
Further done in "Mitefall" where Batmite thinks the shows Jumped the Shark and needs a Darker and Edgier replacement. And the new Batman series, starting next year, called Beware The Batman is just that!
Ho Yay: "Menace of the Madniks!" is basically a Ho YayLove Triangle between Ted Kord and his two friends, Batman and Booster Gold. That may just be a Fandom Nod, since Ted looks slightly awkward all the times Booster hugs him.
Jumping the Shark: The final episode "Mitefall!" has Bat-Mite attempt to invoke this, because he's gotten tired of BATB's comedic formula and wants a Darker and EdgierBatman toon. He alters the series to hit all the classic JTS marks (including having Ted McGinley Other Darrin AQUAMAN), while Ambush Bug (voiced by the original shark-jumper himself, Henry Winkler) tries desperately to prevent him. Since this is the last episode, Bug and Batman ultimately fail to save the show, but at least they make sure it goes out with its dignity.
Ironically enough for the viewer, Bat-mite's changes almost makes the show So Bad, It's Good in how silly the show becomes, including with NEON TALKING SUPER STREET BAT LUGE!
Memetic Badass: Jenny Jones. This thread◊ (NSFW) takes a bit of Comedic Sociopathy in regards to a comment she made about Red Tornado and shows her as a complete brat that belittles everyone for her own enjoyment. Then it goeson from there to the point that it takes The Power of Love, the combined force of about everything ever, and a second thread◊ to defeat her once and for all. .
Considering one of the posts that didn't make it into the second thread screencap had her identified as the daughter of the Anti-Spiral, as well as a brief reappearance to call on her brother to avenge her, it's probably not over.
She basically shows up as a constant annoyance every so often these days.
Moral Event Horizon: Psycho Pirate basically eats the rage of children, Batman is so disgusted at this, he's enraged; then again, that much should be obvious.
"Powerless", Captain Atom flies a jet into the middle of Washington DC and uses it to crash into Major Force. Using lethal force to stop a powerful and seemingly unstoppable opponent in a desperate situation is certainly a difficult choice, one that should have been better addressed in order for the scene to work, but to have the "hero" collide a plane into his enemy, let alone on the soil of the United States Capitol, and then to have Batman compliment his strategy just feels so wrong, especially on the ten year anniversary of the 9/11 attacks.
Though unlike AQUAMAN, that's basically a thematic continuation of his brief appearance (as Expy Devil Ray) in JLU, where he's Too Cool to Live.
The Terrible Trio; they went from rich guys who rob banks to Bloody Roar style kung fu villains in this series.
Crazy Quilt has been a joke in comics for decades, but the show is returning him to his roots as Robin's personal archenemy and a legitimate threat.
Now Crazy Quilt's spot as Joke Character is taken by Kite Man.
Also, Bat-Mite. Can't go wrong with being voiced by Paul Reubens and breaking the fourth wall constantly. That is, until...
The Scrappy: Bat-Mite was the in-universe cause of the series' cancellation. Why? Because he wanted a Darker and Edgier show. Not many people were very fond of him after that.
Screwed by the Network: "The Masks of Matches Malone!" episode has not yet aired in the US, after much attention was given online to the innuendo in the Birds of Prey song.
What's more episode are broadcast with no regularity whatsoever, there can be months between two consecutive new episodes.
Seasonal Rot: The third and final season. Batman became more of a Canon Sue and the stories lost a bit of edge in terms of fun and often got more plot holes.
Some see the third season as being just as good as the other two seasons and enjoyed the appearances from Superman as well. For a lot its the earliest episodes that are a bit shakey.
They Wasted a Perfectly Good Plot: The last Darkseid Invasion episode. Batman is lying on the ground, broken and dying, Darkseid had effortlessly defeated him. We could have FINALLY seen Superman in the show coming to Bat's rescue and doing the most famous fight in DC. Instead, we got a Deus ex Machina with Question reversing the Boom Tubes.
The Scooby Doo crossover. They chose to spoof The New Scooby-Doo Movies (known for their cheesiness and cheap-looking animation) rather than Scooby-Doo! Mystery Incorporated.
The episode "Time out for Justice!" We have an explaination for all the times Batman time travels? Nope. Instead we get a Jerkass Rip Hunter who is not Booster Gold's son. Booster does not get a chance to Take a Level in Badass. So many opportunities, so many let downs.
Actually, the time travels are explained in "The Last Bat on Earth". Professor Carter Nichols has a time travel machine that Batman uses often.
Ugly Cute: Platelet from "Journey to the Center of Batman!"
They fixed her in the second episode she appears in.
Unfortunate Implications: "Return of the Fearsome Fangs". Out of all the students in the dojo, the only one the old master couldn't stand was the black one, despite three others being essentially jerks.
He didn't seem to like any of them, to tell the truth. It was more like Tiger was the the one who couldn't stand the master or at least put up with his crap until he graduated.