Here's the revised and expanded Second Draft:
The Master List
Aaron Langstrom (Son of Man-Bat. His knowledge of the secret was established in Gotham Knights #45)
Alexander Luthor (Dead. Apparently learned during the long period when he had nothing better to do in the paradise dimension than play peeping tom, watching events in the Post-Crisis DCU)
Alfred Pennyworth (Different versions have been told of how he learned, but either he was already working for Bruce when the Batman identity was created, or else he was hired later and quickly found out)
The Appelaxians (Were able to find and invade the Batcave and capture Batman in JLA: Year One based on information gleaned from the Martian Manhunters secret files. Of course, I dont know if the general plot of JLA: Year One is still in continuity in the Post-IC DCU. The roster of founding members of the JLA has retroactively been changed again, after all)
The Atom II (Ray Palmer. His ex-wife Jean Loring definitely knew in Identity Crisis #7 that Bruce is Batman; presumably she heard it from him Ill go back and reread IC later to double-check on how much Ray appeared to know)
Azrael (Jean Paul Valley. Learned during the Sword of Azrael miniseries)
Bane (Figured it out very quickly in Knightfall after looking at Bruce Waynes body language)
Batgirl III (Cassandra Cain. Learned when, for the first time, she saw Batman in his role as Bruce Wayne during the Bruce Wayne: Murderer? event. She recognized his body language instantly)
Benedict Asp (Learned in Legends of the Dark Knight #61. Then he died)
Bird (Now believed dead. Bane told him in Knightfall)
Black Canary II (Dinah Lance. Her current knowledge was recently confirmed in the JLA: Crisis of Conscience story arc, although a few years earlier, in Bruce Wayne: Murderer? she clearly didnt know Bruce was Batman)
Black Lightning (Jefferson Pierce. Learned in Batman and the Outsiders #13. Still knew in a comic published in 1996, so Im figuring that the other Outsiders from #13 still know as well, despite the other retcons of COIE and Zero Hour and so forth)
Blue Beetle II (Ted Kord. Dead. I think he learned in Countdown to Infinite Crisis and then promptly got himself killed)
Booster Gold I (Michael Carter. Dead)
Cain (David Cain. Not sure just when he realized)
Carleton LeHah (Learned during the Sword of Azrael miniseries)
Catwoman I (Selina Kyle. Bruce voluntarily told her during Hush we dont know for sure if she already knew or suspected; we can fill in the blanks any way we please!)
Chronos I (David Clinton. Found out the secret IDs of Batman and several other JLAers a long time ago, according to an Identity Crisis retcon. Then got mindwiped by Zatanna. Then Despero recently helped him rediscover those memories in JLA: Crisis of Conscience. Then they got wiped out (or suppressed, or whatever) by Zatanna all over again . . . until further notice?)
The Crime Doctor (Bradford Thorne. Dead. Learned in his first appearance, in Detective Comics #494. One issue later, he went into a coma from mercury poisoning. Years later, he recovered. Since that time, I gather that no Post-Crisis story has ever clearly told us that he did or didnt remember Batmans identity after he awoke.)
Damian (Batmans newly-introduced long-lost son. Presumably he has known all his life, thanks to his mommy, Talia.)
Deacon Blackfire (Dead. Learned during the miniseries The Cult. That mini has reportedly been erased from continuity, however.)
Deadman (Boston Brand. Since he is normally an invisible and intangible ghost who can go anywhere and spy on anyone, it would be very easy for him to learn any secret identity if he got interested enough to bother, and he demonstrated his knowledge of where to find the Batcave (right under Wayne Manor, natch!) in Batman #530)
Deathstroke the Terminator (Slade Wilson. Probably learned from Terra I around the time of The Judas Contract. Or, even if Terra only knew Dick Graysons real name after she became a trusted member of the Titans, which is the interpretation that Denny ONeil later preferred from the mid-90s onward regarding how much Dick ever shared with his fellow Titans about the Batman Familys secrets, that would be still enough of a lead for a smart guy like Slade to figure out the rest of it himself, later)
Deathwing (Comes from an alternate future timeline, now defunct, in which he had been brainwashed by the Time Trapper so he could pass himself off as Dick Grayson, the Nightwing of ten years from now. Evidently he was well-briefed on all Titans lore and Dick Graysons biography in particular, including the role of Bruce Wayne/Batman in his life, in order to carry the role with conviction)
Despero (Restored various suppressed memories to the Secret Society of Super-Villains in the JLA: Crisis of Conscience story arc . . . and as it turned out, those memories included the knowledge that Batman is Bruce Wayne (not to mention several other JLA secret IDs). In the process, Despero apparently learned this secret himself (if he didnt already know? He is a telepath, after all). At the end of the arc, he was subdued by Zatannas magic and allegedly was going to be taken off to Oa for containment, but as far as I can tell he still had all that knowledge of secret IDs inside his head. The other villains whom he had helped to regain these memories included: Chronos, Felix Faust, Floronic Man, Matter Master, Star Sapphire, The Wizard)
Doc Creasey (Dead. Bought the secret of Batmans identity from The Nobody in Shadow of the Bat #13. One of Jokers henchmen killed Creasey before he could make any use of his new knowledge)
The Elongated Man (Ralph Dibny. His knowledge was recently confirmed in the JLA: Crisis of Conscience arc)
Faith (According to recent issues of JLA Classified)
Felix Faust (Found out the secret IDs of Batman and several other JLAers a long time ago, according to an Identity Crisis retcon. Then got mindwiped by Zatanna. Then Despero recently helped him rediscover those memories in JLA: Crisis of Conscience. Then they got wiped out (or suppressed, or whatever) by Zatanna all over again . . . until further notice?)
Flash III (Wally West)
The Floronic Man (Jason Woodrue. Found out the secret IDs of Batman and several other JLAers a long time ago, according to an Identity Crisis retcon. Then got mindwiped by Zatanna. Then Despero recently helped him rediscover those memories in JLA: Crisis of Conscience. Then they got wiped out (or suppressed, or whatever) by Zatanna all over again . . . until further notice?)
Fritz (A thug who worked for Benedict Asp. Learned in Legends of the Dark Knight #61. Then he died)
Geo-Force (Brion Markov. Learned in Batman and the Outsiders #13)
Green Arrow I (Oliver Queen. Already knew by the time of a conversation with Batman in Green Arrow #5 (the third series of that name). Im told that it is far from clear just when and how he found out in the modern continuity, however)
Green Lantern #whatever (Hal Jordan, formerly known as Parallax, and later as The Spectre II. His knowledge was confirmed during the recent JLA: Crisis of Conscience story arc)
Halo (Violet Hunter. Learned in Batman and the Outsiders #13)
Harbinger (Lyla, the former assistant to the Monitor. Had access to information about everyone interesting)
Harold Allnut (Dead. Presumably found out shortly after Batman met him and took him home to the Batcave in Batman #458.)
Hawkman (Carter Hall. His knowledge was recently confirmed in the JLA: Crisis of Conscience arc)
Hawkgirl (Kendra Saunders)
Henri Ducard (One of Bruces old teachers; he deduced the secret in the Blind Justice story arc, which has allegedly been erased from continuity, which would certainly explain why I dont remember ever seeing Ducard make any use of this knowledge in any subsequent appearances in other comics)
Hourman III, from the 853rd Century (Dead. The secret was also known to a bunch of his friends from the Justice Legion who appeared in the DC One Million event, because the identities of modern-era heroes are all available in public records in the 853rd century)
Hugo Strange (kinda-sorta-sometimes thinks he knows, but -- as far as I can tell in the modern continuity -- has never actually proven it for sure. For instance, he's never captured Batman and then ripped off his cowl to reveal the face of Bruce Wayne underneath)
Hush (Thomas Tommy Elliot. We learned at the end of Hush that he had learned it from Riddler in a conversation we never saw, before that story arc even started)
Ion (Kyle Rayner, formerly Green Lantern #whatever. Learned in JLA #50.)
Jack Drake (Dead)
Jason Todd (Formerly Robin II, later The Red Hood II. More recently Nightwing #whatever -- Im not sure if he still uses that name today, and Ive lost track of what the numbering would be, given that Power Girl and Cheyenne Freemont have also been using that name in OYL stories)
Jean Loring (Refers to Batman as Bruce in Identity Crisis #7)
Jeannie Bowen (In the Blind Justice story arc, which has allegedly been erased from continuity)
Katana (Tatsu Yamashiro. Learned in Batman and the Outsiders #13)
Kathy Sutton (Wife of Red Tornado II. Demonstrates her knowledge in Justice League of America #1 (the newest series; the one that just started a couple of months ago)
Lady Shiva (Nightwing commented that she was on the list of enemies who definitely knew, in a conversation he had with Robin III (Tim) in Gotham Knights #8. I dont think we know just when or how she found out)
Leslie Thompkins (In the current continuity, an old friend of the family who found out soon after Bruce invented his new identity.)
Lois Lane (Probably learned from her husband Clark, but Im not sure just when)
Man-Bat (Kirk Langstrom. His knowledge was established in Gotham Knights #45)
Martian Manhunter (Jonn Jonnz. May have learned by telepathic prying in JLA: Year One if that is still in continuity)
Matches Malone (Dead. But he had somehow figured it out before he died, according to a letter column in Detective Comics #765)
Maxwell Lord (Dead. Apparently learned the secret from Brother Eye, or perhaps by telepathic prying?)
Metamorpho (Rex Mason. Learned in Batman and the Outsiders #13)
Neron (Can see anywhere. Visited the Batcave in Underworld Unleashed #2)
Nightwing I (Dick Grayson, formerly Robin I and Batman III)
"The Nobody" (Dead. A convenient label for a homeless man, real name unknown, who learned Batmans identity and then was killed by the man he sold it to (Doc Creasey), in Shadow of the Bat #13)
Nomoz (Learned during the Sword of Azrael miniseries)
Nyssa Raatko (AKA Ras al Ghul II. Dead. Demonstrated her knowledge of Bruces secret in the Death and the Maidens miniseries. I dont recall that we ever learned how she knew)
Oracle (Barbara Gordon, the former Batgirl I. Shes known for a long, long time, but Im not certain exactly when and how she found out. I dont know if theres ever been a Post-Crisis flashback story that gave us the current official details. In Pre-Crisis Earth-1 continuity, Bruce told her voluntarily in the 70s, then her knowledge later got mindwiped in an incredibly bad story, then in Detective Comics #526 Gerry Conway delicately retconned that by simply having Babs Gordon (still Batgirl I at the time) casually tell Dick that she had deduced their secret identities months earlier but, when she realized how uptight they were about their privacy, she tactfully permitted them to think they had managed to throw her off the scent. As far as I know, Conways version can still be considered valid in the Post-Crisis DCU, unless a newer story has explicitly rewritten the details of how Babs found out? If you know of such a story, tell me!)
Owlman (Thomas Wayne, member of the Crime Syndicate of America, on the Earth in the Antimatter Universe. Introduced in Grant Morrisons JLA: Earth-2. Once he visited the regular DCU Earth, it was a foregone conclusion that hed figure it out. Since he is effectively Batmans evil twin from a parallel universe, as soon as he became aware of Batmans existence he couldnt help knowing that Batman must be a member of the filthy rich Wayne family of Gotham City, which would narrow the field down to one possible suspect, right?)
The Phantom Stranger (He seems virtually omniscient. In Batman/Phantom Stranger he dropped in on Bruce Wayne and his conversation made it clear he knew)
Plastic Man (Eel OBrian. Learned in JLA #50)
Ra's al Ghul (Dead. Already knew the secret, from behind-the-scenes detective work, when he made his debut way back when in Batman #232. At least some of his Ubus and other hirelings have also known, when it suited his purpose to let them know)
Red Tornado II (Not sure when he learned in modern continuity, but probably before JLA: Crisis of Conscience when Batman is working to repair him in the Batcave)
Riddler (Edward Nigma. At the very end of Hush, revealed that he had already figured it all out, behind the scenes, before Hush ever started. Now, however, he appears to have totally forgotten or else is pretending he forgot in Dinis current run on Detective Comics.)
Robin III (Tim Drake. Revealed that he had already known for several years before he ever got around to mentioning his knowledge to Dick Grayson and Bruce Wayne during the story arc A Lonely Place of Dying in 1989)
Roy Kane (Dead. Learned and died in the Blind Justice story arc, which has allegedly been erased from continuity)
Ruby (Apparently her real first name. Dead. A female criminal who broke into the Batcave in Batman #577 and learned Batmans secret identity and then conveniently died by the end of the issue, as did her accomplices, Rubys Brother and Sneaky Pete.)
Ruby's Brother (Dead. We never knew his real name. See entry for Ruby)
Sasha Bordeaux (Learned in Detective Comics #756 when she found one of Bruces costumes)
Sentinel (Alan Scott, formerly the Golden Age Green Lantern. Showed that he knew in Detective Comics #784)
Sherlock Holmes (Showed that he had deduced it independently in Detective Comics #572. As far as I know, theres no reason to think thats been retconned)
Shondra Kinsolving (Learned in Legends of the Dark Knight #61. Then she regressed to early childhood, mentally, and was placed in a sanitarium. In Hush there was a brief reference to the vague idea that eventually she got better. She may or may not remember anything about Batmans secrets now; who knows?)
Silver St. Cloud (Learned during the Steve Englehart/Marshall Rogers run on Detective Comics that is reprinted in the TPB Batman: Strange Apparitions)
Sneaky Pete (Dead. See entry for Ruby)
The Spectre I (Jim Corrigan. Dead and gone, now. Visited the Batcave in Batman #541.)
The Spectre III (Crispus Allen. Apparently learned in #1 of his own series)
Spoiler (Stephanie Brown, AKA Robin IV just before she died. I think she would have learned Batmans identity when she became the new Robin, or possibly sooner?)
Star Sapphire IV (Deborah Camille Darnell. Dead. Found out the secret IDs of Batman and several other JLAers a long time ago, according to an Identity Crisis retcon. Then got mindwiped by Zatanna. Then Despero recently helped her rediscover those memories in JLA: Crisis of Conscience. Then they got wiped out (or suppressed, or whatever) by Zatanna all over again . . . until further notice?)
Superboy-Prime (Clark Kent of Earth-Prime, which is supposed to be our Earth. Presumably he knew from a very early age, thanks to comic books, TV shows, etc.)
Supergirl #whatever (Kara Zor-El, the Rebooted Version)
Superman (Clark Kent, Kal-El)
Supernova (Established in "52")
The Synaptic Kid (Only appeared in Detective Comics #633. Learned Batmans identity telepathically, then after a very confusing story apparently ended up in a comatose condition with a mental breakdown, as a result of the shocking experience of messing around inside the complexities of Batmans head without an invitation to be there. Let this be a lesson to us all . . .)
Talia
Trogg (Bane told him in Knightfall)
Tsunetomo (Dead. One of Bruce Waynes martial arts teachers. Recognized Batmans fighting style in Detective Comics Annual #3)
Waverider (Learned all sorts of secrets, including Batmans identity, when he was examining the possible futures of different heroes during the Armageddon 2001 event in 1991)
White Martians (According to a statement made in the JLA: New World Order story arc, there are 78 of them. In the JLA: Terror Incognita story arc, it became clear that with their telepathy and all that, they definitely knew Batmans secret identity, among others)
The Wizard (William I. Zard. Found out the secret IDs of Batman and several other JLAers a long time ago, according to an Identity Crisis retcon. Then got mindwiped by Zatanna. Then Despero recently helped him rediscover those memories in JLA: Crisis of Conscience. Then they got wiped out (or suppressed, or whatever) by Zatanna all over again . . . until further notice?)
Wonder Woman I (Diana. Apparently it is not crystal-clear just when she learned)
Zatanna (Zatanna Zatara. Her knowledge of his identity was recently confirmed during the JLA: Crisis of Conscience story arc when she visited the Batcave and called him Bruce while trying to apologize for mindwiping him many years ago (as previously revealed in a retcon flashback in Identity Crisis). She offered to do anything she possibly could to make it up to him, and Batman listened to her speech and then simply told her to leave. (Considering that he didnt hit her, file criminal charges or a civil lawsuit against her, scream obscenities at her, or suggest she go mindwipe herself and her former co-conspirators to balance the scales by removing their memories of his secrets this time around, I thought he handled it rather well.))
Zombie (Bane told him in Knightfall)
(By the way, the notes at the bottom of the first draft still apply. They explain some of the choices I made in who to leave off, for instance.)