Batman
1) Scarecrow finally makes a type of Fear Toxin that works on Joker. After using it, however, he begins to have regrets.
2) When a new villain comes to Gotham and messes up the status quo, the Rogues must get rid of them before Batman comes back from vacation/being sick/whatever.
3) No one, not even Alfred, dares disturb Jason's room after his death. Because of this, they don't realize that he's moved back in.
Bonus: He steals food from the kitchen at night, and someone's convinced it's a ghost doing it.
4) When someone frames (a non-murderer) Riddler for a series of deathtrap-related deaths, he decides to show them what a deathtrap designed by him really looks like...
5) When Scarecrow calls Mad Hatter a pet name for the first time, Jervis's brain shorts out from joy. Unfortunately, this happens in the middle of a heist/fight/scheme.
6) Someone decides that Joker's obsession with Batman is hurting the clown, so decides to help him get over it. The twist? It works.
7) Riddler gets bored/frustrated and makes the riddles to defeat his traps just mocking questions.
(Examples; 'Riddle me this: why does your nose look so weird?', 'did you actually choose that hairstyle or is there some fucked-up dress code I didn't know about?', 'if you want to escape, you must answer this question: what are your top three most embarrassing moments?')
Based on a DnD sketch.
8) There are many fics where Lock-Up meets Joker and Bolton comes to regret it — but what if it was the other way around instead?
Bonus: The other Rogues unexpectedly come to Joker's rescue.
9) A new therapist tries using shock collars to train the Rogues out of their compulsions. For some of them it actually works, leading them to question whether the abuse was justified.
10) Under the influence of the Lasso Of Truth, Riddler tells Wonderwoman exactly how to stop his plot — it's not his fault she can't understand him.
(AKA: Riddler has no need to lie, he has riddles and wordplay on his side)
11) The basic plot of Batman Forever, but with the BTAS versions of the characters. Or a different Batman movie with BTAS characters.
12) Catwoman and Penguin end up disrupting each other's heists while trying to steal the exact same item for the exact same reason; a gift for the other.
Bonus; Riddler is close to both of them and gets pulled into both plots, sworn to secrecy by each, and must deal with the chaos.
13) Harvey Dent and Temple Fugate were both lawyers once. Do they ever bond or fight over that? Did they ever face each other in court, before they were Twoface and Clock King?
14) Harvey and Harv must work together without their Coin to stop a third personality that only comes out when they use it.
15) Clock King thinks while making paper clocks in Arkham.
16) When a semi-pacifistic but still chaotic Joker falls out of a wormhole, Jason must deal with a version of his murderer who's more scared of Jason than Jason is of him.
17) Jason decides to announce his resurrection by sneaking into the manor and falling asleep on Bruce's bed.
AKA: Bruce wakes up to see his dead son sleeping peacefully next to him. He doesn't react well, then he does.
18) Jason's in a fight, and the only available weapon is a crowbar(/crowbar-like object). Angst.
19) Damian keeps a journal of all the 'rules' he's learned since coming to live at the Manor (and the 'orders/punishments' he's received). It's found.
Some horror is felt, some laughs are had, and some misconceptions are righted.
AKA: Damian misunderstanding how not-assassin life works.
20) Damian keeps notes secret by writing them in code in one language, with the letters of another, and the grammar structure of a third. Even his Father would have trouble reading it.
A sleep deprived Tim takes a while to realize that the reason Damien's staring at him like that is because the thing he's casually reading out of boredom is supposed to be difficult to understand.
Whoops.
(Possibly related to above idea)
21) A hero starts operating in Gotham solely during the day. It takes the Bats an embarrassingly long amount of time to realize this.
22) Instead of beating Tim up, Jason kidnaps him so no other kid will face his fate. This one change in decision changes everything.
23) People — Cops, civilians, other heroes, Rogues, etc — witnessing the Batkids just being siblings.
From arguments to in-jokes to comfort hugs to teasing to flat out saying 'I love you', this is one bat secret that doesn't remain secret for long.
24) Bruce captures Red Hood and keeps him on house arrest in the Batcave while administering therapy. Jason is very much not okay with this... Until he is.
25) Justice League comes to Gotham without Batman's permission. The Rogues show them why they need Batman's permission.
AKA: Even Superman can't resist Ivy's pollen, Flash isn't a match for Mr Freeze, and Wonderwoman really shouldn't have tried lassoing Riddler (he is telling her the location of the 'bombs', it's not his fault she isn't smart enough to understand what he's saying). J'onn J'onzz vs Firefly does not in well.
Bonus: The Justice League is in a pretty bad spot before Batman shows up and just handles these monsters as if they were nothing.
26) Tim is going to do something that the others wouldn't approve of. Red Hood finds out and tries to stop him, which should be easy considering the younger definitely can't take him in a fight.
Tim uses his knowledge of Jason's triggers to prove how very wrong that idea is. Bonus if Tim leaves Jason unable to fight without actually laying a hand on him. Featuring guilt from Tim.
27) When one of Tim's parents hits him, Bruce predictably reacts with fury. Less predictably, so do some of the Rogues.
AKA: Rogues with backstories involving abuse from parental figures find out that the third little bird's parents aren't the greatest, and decide to do something about it.
Alt: After Tim gets kidnapped, one of the Rogues notice a black eye and question him about it. When he dodges the questions, they angrily think that Batman's the reason. Tim hurriedly confesses that it was one of his parents, leading to an unexpected quest of vengeance and the strangest found family Tim's ever been part of.
Alt: Oooh, Tim stalks and joins the Rogues instead of/along with the Bats??
28) "Would you cut that out?!" Jason screeches, but the witch just turns another one of his bullets into a strangely soft mechanical duckling.
Or; A witch gets bored while on vacation in Gotham, so she spends her week messing with Bats and Rogues alike.
29) A new non-native-gothamite mayor decides to prevent his daughter's beloved school from closing by assigning Rogues as teachers.
AKA: A new mayor comes to Gotham. He is not native. His daughter really likes her quirky highschool, but it is going to be shut down due to lack of teachers.
The mayor has a 'brilliant' idea. Don't a lot of the Rogues have PHDs or are otherwise hyper intelligent? He starts a new reformation program.
Cue the Rogues being stuck as highschool teachers with tracking anklets. To their surprise, it isn't too horrible, mostly because the students are crazy.
In fact, a lot of the students are meta or batkids. They've been waving a secret super war for the past couple of years.
The Rogues find themselves the reluctant mentors to the next generation of super heroes and villains.
//There's staff there to watch them. Including a very unfortunate headmaster (who may be just as crazy as they are)
30) Batman White Collar AU — Joker gets placed in someone's custody in an experimental new program, complete with tracking anklet. Harley is Mozzie.
Bonus: Edward Nygma as Burke.
31) There are many Kings in Gotham, but only one its Fool cares about. Joker meets the city's various self-proclaimed monarchs, including its true King; Bruce Wayne.
32) Joker learns that Jason has trouble around loud laughter, and decides to fix it. The fact that the kid has severe trauma based around the clown doesn't occur to him until after he's kidnapped him.
33) Tim loves to laugh, in all sorts of ways. It's caused issues, gotten him compared to Joker or just not taken seriously, but it's never been that big a deal.
Until Jason's resurrected, and the second Robin has various and horrible reactions to different kinds of laughter.
34) Brucie Wayne — in all his giggling, airheaded glory — mercilessly flirts with Joker, leaving the clown flustered and confused.
Bonus: Then Batman makes a reference to something Brucie said, and Joker's mind is too fucked for him to remember he's in the middle of an evil plan.
AKA: Bruce has found his new favorite game, and Joker's feeling a whole lotta things about it.
35) Jason is shown a montage of what, exactly, happened after he died. Bruce breaking, everyone splintering, Tim stopping it. He reconsiders a few things.
(Bruce trying to kill Joker. Bruce leaving Joker to die. Bruce barely not killing every criminal he came upon. Bruce and Dick and Alfred all splintering. Tim forcing himself into the spot of Robin, despite not being wanted and not really wanting to, just to fix things.)
(His Replacement saving his family.)
36) When Twoface's sides get split into two people, their romantic partner must choose between them.
I'm thinking Tworiddle, but it honestly works with any Twoface ships.
37) High Potential AU but with Riddler as Morgan.
(If you haven't watched High Potential, go watch it, the main character is pretty much civilian!female!Riddler)
38) Edward Nygma (under an alias) gets a civilian job as a cover. While there, he wows his coworkers by easily solving Riddler's riddles.
(He only solves the ones repeated on the news, to explain how he knows them in the first place).
Bonus: Edward is known for insulting Riddler's 'easy' material, prompting others to worry that he will get kidnapped by the villain. One person actually tries to warn him about it...
Bonus bonus: ...leading him to stage and televise his own kidnapping, upstaging his criminal identity. Meanwhile, Batman is sooo not dealing with this nonsense.