Since I only recently started reading comic books on a regular basis, this question has only recently crawled into my brain
Hush and Ra’s al-Ghul seem to have displaced the Joker as Top Threat to the Batman’s Well Being. Both of them know that Bruce Wayne is the Batman IRL. So far, they both seem to be keeping the secret to themselves, but that could change.
What other comic-book type heroes have dangerous enemies who know what they do on their day jobs? Does Lex Luthor know that Superman is Clark Kent, Mild-Mannered Reporter for the Daily Planet? What about Spider-Man? Any of his favorite arch-villians know he’s really Peter Parker?
And while we’re on the subject, in the canonical DC stories, does Jim Gordon know that Bruce Wayne is really the Batman?