The episode "Payback" deconstructs Bully Hunter. The episode features a masked Vigilante Man who specifically targets adults (parents/teachers/bosses) that bully various teenagers in Gotham City. It’s clear that he’s going overboard, as his attacks on them are rather violent and almost lethal against those who've slighted others. It’s revealed that Payback is the son of a doctor at a local youth counseling center, who was depressed that his father was spending too much time counseling other teenagers and neglecting him and decided if the source of the teens' troubles disappeared, he'd have more free time.
The episode "Heroes" deconstructs Freak Lab Accident origin stories. A team of Fantastic Four expies discover that the high radiation levels from the accident that gave them their powers is slowly killing them and driving them insane, and said "accident" was orchestrated by their old colleague in a Murder the Hypotenuse scheme. It's a chilling reminder that the line between hero and villain can be as slim as the choice one is offered. The leader even admits he's not a hero because the accident robbed him of any real choice to be one or not.
The episode also briefly deconstructs the Celebrity Superhero: they're so popular with the public and work so well with the government only because the military has taken them in as personal attack dogs, and is trying to make sure they have a good public image.
The Kid Hero trope is deconstructed in Batman Beyond: Return of the Joker. Being a youngster who fights evil won't spare you from the torture and brainwashing Mind Rape you'll receive once you end up in the claws of a sadistic, murderous, amoral psychopath. If you do survive it, you'll completely lose your sanity, it will take years of therapy to cure you, and you have to live with PTSD through the rest of your life. Though Tim was actually not regretful of it until the Joker began influencing him in his attempt to take over.
Timothy Drake (as an adult): Fun and games. Boy wonder playing hero. Fighting the bad guys and no one ever gets... Oh god. I killed him. I didn't mean to. I tried so hard to forget. But I still hear the shot. Still see the dead smile. Every night the dreams get stronger... He's there when I sleep. Whispering! Laughing! Telling me I'm just as bad as he is! We're both the same!note Though his 'dreams' are actually the result of the Joker placing a microchip on him before he died, in an attempt to take over Tim's body.
The Joker points out that for all the fear he invokes being The Cowl, Batman is not more than (in his opinion) a pathetic Manchild crying out for mommy and daddy after all those years.
The Joker: And kind of like the kid who peeks in at his Christmas presents, I must admit, it's sadly anti-climactic. Behind all the sturm and bat-o-rangs, you're just a little boy in a playsuit, crying for mommy and daddy! It'd be funny if it weren't so pathetic.
Tim: We gave our best, but in the end that wasn't good enough for the old man. When I was younger, part of me thought I would go on and on, and someday...ah, capes, costumes, playing hero - it was kid's stuff! Bruce probably did me a favor. In the end, I was so sick of it I never wanted to see that stupid Robin suit again...!
However, it's been noted that his hatred for being Robin was a result of the Joker's influence on him and he was actually pretty okay.
Card-Carrying Villain is Deconstructed by Terry during the finale of ''The Return of the Joker". As much as the Joker tried to be Affably Evil to Batman and get him to laugh, he was really Faux Affably Evil. He never made Batman smile, laugh, or take him seriously as a comedian, which Terry guesses is why he became obsessed with Batman. When Terry decides to start playing the Joker's own game of taunting and telling jokes (basically being The Heckler), the Joker has a Villainous Breakdown, as Terry points out his humor flat out sucks.
Terry McGinnis: The real reason you kept coming back was you never got a laugh out of the old man.
The Joker: I'm not hearing this...
Terry McGinnis: Get a clue, clowny! He's got no sense of humor! He wouldn't know a good joke if it bit him in the cape... not that you ever had a good joke.