Batman Beyond/WMG

The Beyond Suit and Bruce's training is at least in part a tribute to Dick Grayson (as Nightwing).
Don't know if this has been noticed, but check the design of the suit. Very similar to the Nightwing outfit. It's been shown that Bruce and Dick never reconciled, and its understandable if Bruce considers that a failure and is trying to make up for it by training Terry. Terry himself shares a lot with Dick (and other teen superheroes) with his attitude and sense of humor (we are shown that he's fundamentally different from Bruce in that he likes to talk )), except he's still fairly dark and serious (like Nightwing, compared to Robin). It can't be definitively known if Bruce's training would have had any effect on this, but its not too much of a stretch to think that Bruce acknowledge's some of Dicks better points (he is kind of a young Ace in the DCU) and try to instill those into Terry.
 * He also played by the JL's rules, tried for teamwork, and won their trust in decent time. Bruce was generally a bit more reticent. Of course, Terry's backing down in the end does show that he has some of Batman's loner nature, but it's not defining him like it did with Bruce.

Nightwing was horribly injured.
That's why he quit.
 * Barbara's line seems to suggest that he's still operating though. Otherwise she would have told Terry to "Look up a guy called Dick Grayson."
 * No, she didn't want to assume that Terry knew Nightwing = Dick Grayson. It's bad form to just give out a secret identity, and he didn't know that she was Batgirl until she walked into the Batcave.
 * Except their initial conversation where Barbara told Terry about why she quit being Batgirl started with "So you and Dick Grayson..."
 * That still doesn't make any sense, why would she tell him to look up someone who's not operating under that name anymore? Dick's as good at covering his tracks as Bruce and if he doesn't want to be found he won't. And she told him about Tim pretty easily.
 * Go back and watch Return of the Joker again and pay particular attention to just before the flashback starts. Barbara straight up tells Terry that Nightwing is Dick Grayson when she mentions he'd left for another city.
 * Confirmed. The new comic (2010) shows what happened to Dick.
 * Come now, everyone knows that the Joker is the only one allowed to harm a Bat and let is stick. Not even Darkseid can break that rule. It had to have been the Joker.
 * Besides, Dick wouldn't have come up. Barbara was uncomfortable talking about his near death. They had been close. But the severity of the injuries combined with it not being the impetus for Joker hatred meant it was relatively unimportant. The Joker shot up Dick. These things happen. Birds fly, fish swim, The Joker shoots machine guns at people. But he crossed the damn line with Tim. Anyone who's ever been psychologically tortured will tell you it's WAY better to catch a bullet then to get brainwashed and abused. Plus, Dick was basically an adult. Tim Drake was a kid. Batman has a thing about victimized kids.
 * Besides, Dick wouldn't have come up. Barbara was uncomfortable talking about his near death. They had been close. But the severity of the injuries combined with it not being the impetus for Joker hatred meant it was relatively unimportant. The Joker shot up Dick. These things happen. Birds fly, fish swim, The Joker shoots machine guns at people. But he crossed the damn line with Tim. Anyone who's ever been psychologically tortured will tell you it's WAY better to catch a bullet then to get brainwashed and abused. Plus, Dick was basically an adult. Tim Drake was a kid. Batman has a thing about victimized kids.

Nightwing is still operating.
Why would Barbara tell Terry to go looking for someone who doesn't exist anymore? Dick simply changed his costume to keep up with the times, and Bruce just put the old one on display because he likes to keep things. It's not like Nightwing was identified solely with Batman; he's a fairly well known and respected superhero in his own right, and in the mainstream comics he's pretty much considered the linchpin that holds the whole damn mess together. There isn't a single superhero that wouldn't answer his call or bow to his experience, and yes, that includes Superman and Batman.
 * Jossed if the latest comic book is taken into account.

The chair was evil
It's obvious.

Aquagirl is Arthur Jr.'s daughter
The Aquaman seen in the picture in "The Call" has his old look, rather than the new one he got fortysomething years earlier. Also, he had a son back then. Do you really think he would have two kids with an age difference of a few decades?

Obviously, the Aquaman seen in "The Call" was the new Aquaman, aka the old one's son, Arthur Jr, aka the guy whose dad cut his own hand off when the evil uncle nearly had him killed. Retcons apply to animated adaptations of comic books, too.

Bruce has a liver disease
His eyes look jaundiced. That generally means liver disease (such as Hepatitis, liver failure, etc.).
 * They pulled something similar when they redesigned Commissioner Gordon in the earlier series. Bruce does have obvious heart problems that could contribute to that.
 * Also, doesn't Bruce sport "liver spots" on his hands?

Mad Stan was originally part of The System.
More specifically, he was the Chief of the Army. After being fired by the Vice President for nearly starting a war with Mars, he became disillusioned with the establishment and its incompetent leaders and made them his new enemy. This is the only thing that changed about him.

Terry's younger brother will be Robin
It's bound to happen sooner or later. He will be inspired by his older brother, Terry, to the point that he might end up wanting to be a superhero himself and assist him.
 * Executive Meddling actually tried this at one point (except making Matt Kid Batman instead of Robin). Thankfully, it didn't work out.
 * Kid Batman would have sucked, but Matt as Robin could have been awesome.
 * Matt LOOKS like Robin. Grow him about a foot and give him a costume, he's Tim Drake. Minus the dead da... Well, he doesn't have the hyperactivi...oh. Shit. I think he might be Tim Drake. Oh well. Could have been Jason Todd. THAT would suck.
 * This troper accepts this as his personal canon. And it happened some time between the series and "Epilogue". He could very well take on the name "Red Robin".

Max will be either Robin or Oracle
She already helps out sometimes with the research part, which makes her fit the Oracle role. On the other hand, if she ever gets a strength-enhancing suit like Terry she could conceivably become Robin.
 * Or Batgirl.
 * I was praying for this when I first watched Batman Beyond. Although, for some reason it seems like she would be sexier in the Robin style costume...
 * No I do not want to analyze what that says about me.

Superman knows the truth about Terry being

 * At the end of "The Call Part 2", Clark invites Terry to join the Justice League full-time, and mentions that Bruce had technically only been a part-timer. Terry replies "I guess we have something in common then," as he walks away. Superman quietly remarks "More than you know, son. More than you know."

Now obviously, he could have just meant that Terry had something in common with Bruce in terms of personality, but it's certainly possible that Superman was aware of Terry's true parentage. This is a guy who can see DNA after all.

Consider the fact that in the JLU episode "Epilogue", Bruce had apparently known the truth about Project Batman Beyond for quite some time by that point. It's possible that Superman also found out about Project Batman Beyond at some point but kept quiet about it out of respect for both Terry and Bruce.

Ivy is the father of Harley's children.
Look at the technology in the DCAU.

The Creeper is the father of Harley's children.
Inspired by the above WMG and a never-written fanfic by this troper, look at the facts. The only two people in the DCAU that Harley has sparks with are Pamela and Jack. After working as the Joker's henchgirl for so many years, it's obvious she wasn't going to be able to ever have a normal relationship. Perhaps she just so happened to run into Jack on a blind date or in his alternate persona, Creeper still recognized her scent. She decides that a guy whose similar enough to her last beau without all the abusive qualities is a pretty nice deal and they eventually get married. Thus, it also explains the Dee-Dees offbeat personalities, since some of those toxins and chemicals probably messed up the DNA down the line.

Splicer Technology
Started off from the thing developed in On Leathery Wings that turned an unfortunate scientist into a bat like creature. It has been refined to work for any animal.
 * ...isn't that just canon? or at least heavily implied canon?

The new BatSuit was made for or by Batwoman
Am I the only one who noticed that the bat symbol for Batwoman and Terry are the same? Both share a similar color theme, mostly black with a few splashes of red.
 * At least part of the technology for the new suit is from the suits of the Batwomen in Mysteryofthe Batwoman so it is possible that Bruce took some inspiration from the design as well.

Who is Curare?
Well, let's take a gander. Best assassin in the League of Assassins, female, never see her face - could she be an alternate universe Cassandra Cain? -Who is Curare, in the first place. I can't find a picture of her, on google images.

Ghoul is, in some way, related to Jonathan Crane, the Scarecrow.
Take a look at him. He's pretty lanky and he clearly modelled his costume after him.
 * He could maybe be his son, following in his footsteps.
 * He may have some relations to Penguin. Since his voice actor mimics Christopher Walken's voice. An early script revealed that Max Shreck was Penguin's older brother.
 * He could be related to Roland Daggett (who was originally gonna be Max Shreck).

Ghoul is Carter Wilson AKA Terminal from Hidden Agenda

 * Ghoul and Terminal were both voiced by Michael Rosenbaum (not that that means much in the DCAU), they both had vaguely skeletal Joker paint, both spoke in monotones. Maybe Carter decided to make himself scarier after juvie and adopted the appearance of Scarecrow, who would have been well known to Jokerz members as one of their idol's contemporaries. In one of the tie-in comics it mentions that for a time he was imitating Two Face, so maybe he went through villain "phases".

General Norman from "Heroes" is related to General Wade Eiling.
They both hate super-powered humans and costumed vigilantes. Norman could be Eiling's (illegitimate) son. Or even his nephew who respects him and joins the army in his honor.

Bonk is Bane's grandson.
This is just speculation but I'm just wondering how he was able to match the Batsuit's strength...personally I think it's because Bane was his grandfather.

Grandma Harley is not Harley Quinn.
They just happen to have the same name.
 * Jossed. Word of God says Nana Harley is indeed Harley Quinn.

Bruce (of the main timeline unabused by Chronos) did remember traveling into the future by the time Batman Beyond took place.
And more importantly, he remembered meeting Terry McGinnis and learning he would take up his mantle as Batman. When the two finally met when they were chronologically supposed to, Bruce decided to wait and see how events unfolded. And then Terry stole his batsuit to go avenge his father. In all honestly, he really was going to let Terry get his way and take care of business in the end. He just wanted to make sure Terry learned his lesson about not running off with old Bruce's things behind his back.

The batarangs Terry uses were derived from Rocky Ballantine's programmable metal.
The metal is stored in liquid form in the Batsuit until the wearer performs a specific hand motion, then the metal comes out of the wrist in a pre-programmed form. It can even change color to red and black.

Mad Stan is the son of Lock-Up.
This page pointed this out!

Barbara Gordon becomes Oracle.
After she retires from her job as police commissioner, she becomes Oracle.