Joker said he had been dormant in Tim's mind for years. It's possible that his career path of engineering may have been a subconscious push by the Joker to develop skills that would elevate his return beyond simple street crime.
The New Joker in his introduction scene kills Bonk with a BANG! flag gun. Tim Drake uses that same gun to kill the old Joker. Sort of solves the mystery right there.
Fridge Horror is hard to avoid in the DCAU - they had to follow the rules for kids TV, meaning no killing. This often led to Fates Worse Than Death that the real impact of would not be felt by those watching until they grow up.
Speaking of Batman Beyond, in the JLU BB finale, Amanda Waller picked the exact same kind of parents of Bruce's for Terry's. In the pilot, Terry's parents were divorced. Does that mean that, if Bruce's parents weren't killed, Thomas and Martha Wayne were going to split up?
One fan theory of why they were divorced was the fact that both sons looked nothing like the father.
According to Bruce Timm, Epilogue's revelation was partly motivated by the staff realizing Terry and Matt's black hair is genetically improbable given Mary is a redhead and Warren's hair is light brown - in turn opening the possibility that Warren had suspected infidelity.
Terry McGinnis: It's funny, I know about all your other major enemies but you never mentioned him. He was the biggest, wasn't he? Bruce Wayne: It wasn't a popularity contest. He was a psychopath, a monster.
Considering Robin's Undying Loyalty to Batman, one can only imagine how bad the torture must have been to make him crack and give away Batman's true identity.
Woof the Hyena Joker. It seems the splicing reduced him to a feral, cackling beast incapable of speech. We're never told whether this process was voluntary or not, and even so, what kind of person would want to do this to himself?
He might have come from the other direction—a hyena that was spliced toward being humanoid.
The brilliance comes when tying in another Paul Dini work Mad Love. Mad Love's key factor is playing on the irony that Harley succeeds at everything the Joker fails at. In the climax of the movie, Terry mocks Joker by saying that his fixation to Batman was because he never could get him to laugh. In Mad Love, Harley gets him to laugh completely unintentionally and effortlessly.
Another detail that ties in - at the end of the movie, it's revealed that after the Joker was killed, Harley moved on and started a family, apparently abandoning her life of crime and being angry at the thought of her granddaughters becoming criminals. In Mad Love, we see that much like real life abusive couples, Harley is continuously lured back to crime and the Joker by his little Pet the Dog moments towards her, which keep her from realizing what a horrible person he is (at the end of the episode, for example, she was cursing his name before seeing he sent her a flower). It's likely that with the Joker dead, there was nothing to interrupt Harley's next doubts about him, leading to her rejecting his memory and ideals.
Another reason why she was the best? She got Joker Immunity. He didn't.
There's a problem with the whole Harley besting the Joker in Mad Love interpretation, though: she only succeeded because she followed one of the Joker's plans, a fact she admitted. The Joker had previously rejected it for not being funny, which he considers a requirement for a successful plan: just defeating Batman isn't enough, he must be funny while doing it. Even after the plan succeeded in catching Batman, it still wasn't funny, so the Joker still thought of it as a failure. The Joker had no reason to consider Harley to have succeeded.
Joker didn't know how to make the fish smile. Harley succeeds in making them appear to be smiling. Joker has never caught Batman in a death trap that he couldn't escape from. Harley did on her first solo try. Harley is able to devise a plan all on her own that is far more effective than anything the Joker has ever done. Joker would never consider Harley to have succeed but the readers definitely (probably even Batman) would.
Plus, when he arrived she had to explain the plan and why it was a joke to him.
Joker "If you have to explain a joke, there is no joke!"
I've been watching some of the original Batman The Animated Series episodes (working my way through the entire series). You know what? Joker isn't funny. He makes terrible puns and stupid (and destructive) pranks, but the only thing he ever got a chuckle was when he was singing the Batman Jingle Bells song or saying jokes in a different persona... and neither of those were made by him (at least, in a meta sense). Aside from that, he's only unintentionally funny. -Peteman
This is especially notable when one considers Terry's snide comment about how the Joker might get a laugh if he dropped his pants or something of the like. In the Batman: The Animated Series episode "Make 'Em Laugh", he gets the biggest and only laugh out of Gotham as the Joker when he unintentionally drops his pants after being beaten by Batman.
The movie could be seen as a deconstruction of the character as a clown at all. As much as The Joker bills himself as the Clown Prince of Crime, he's not really a clown beyond his superficial gimmicks as see in the Batman: The Animated Series episode "To Be a Clown" where he impersonates a party clown: he can do some impressive "magic" tricks and slight of hand, but he never actually makes anyone laugh or find anything funny (beyond one clown-obsessed boy who is really more awed than anything). The clown thing is more a convenient theme than anything else, since despite not being funny the Joker is a competent showman in regards to getting and keeping attention and so would choose a theme to let him do that on some level. T
The classic clown tricks he uses as weapons, like the joybuzzer, flower, and so on, are only funny as clown tricks when acted properly, something the Joker doesn't do (he loves drama and terror too much to manage to get laughs), or with a partner who reacts, which the Joker does not have in his chosen partner of Batman. Thus showing how the Joker failed to even see how the items he was using were supposed to be thought of as funny in the first place.
Also, as Terry notes during his heckling, the original Batman really didn't have a sense of humor, so he had no reason to call out the Joker's tricks as not being funny since he didn't find anything funny. Terry meanwhile has a reference point and so can definitively call the Joker out as not being funny.
Dean Stockwell was likely chosen for the role of an adult Tim Drake because of his background as a child actor, but the Joker connection may have been inspired by one of his earliest roles as the lead in "The Boy with Green Hair".