Apparently another one of the unspoken rules of comics is going to be broken.
In Justice League Batman found out who Joker is but couldn't believe the answer. Now it seems much like Wolverine we'll learn an origin we never thought we'd learn a definitive answer for. If Batman can't believe it the answer will probably surprise us meaning it's likely someone we've been introduced to in some capacity. Since Geoff Johns is involved I'm hoping the answer is better than the ones I've seen online.
Thomas Wayne: He's been dead a long time and for him to suddenly be not only alive but his son's enemy would be hard to accept. This would mean Joker was also in his 60s and took on a different build than he had as Thomas. With the idea of Thomas Wayne Jr., Bruces' younger brother, possibly being around it makes this theory especially contrived. DC might take some risks but I can't see them screwing over one of their biggest characters' origins. That would be like Spider-Man finding out Green Goblin was Uncle Ben.
Willis Todd: Dick and Tims' dads were likely guesses too but I've seen this one talked about in length. This would mean Jasons' dad murdered him and his mom which makes DITF worse than it already was. Willis was a henchman type pre-Flashpoint (his role was vague) and a drug dealer post-Flashpoint that was in and out of jail a lot. While there could be some retconning to make the timelines fit better (since he was normal and around when Joker was about) Joker seems far too crafty for Willis. I'd hate to see this connect plus it would make Joker have an even stronger link to Jason than Bruce.
Alfred Pennyworth: This idea has been talked about prior to the ID talk but since Joker cut off his hand it seems even more ridiculous.
I have faith that Johns won't do any of these even if I'm not sure what direction he will take. Something this big needs to be done right, have an impact but not trample on other stories.