I've been working on this for a while, so...
Part 1: Friends & non-costumed allies:
- Alfred Pennyworth: Helped - as depicted in numerous flashbacks - creating the "Batman" identity.
- Dr. Leslie Thompkins: Learned either in Gotham Knights #7 (flashback) or LotDK #21-23.
- Silver St. Cloud: Learned in 'Tec #474 (still in continuity?).
- Sherlock Holmes: Revealed his knowledge in 'Tec #572.
- Dr. Sheila Haywood: probably learned in Batman #427, but died shortly afterwards.
- Henri Ducard: Revealed his knowledge in Detective Comics #600.
- Roy Kane and Jeannie Bowen: Learned in Detective Comics #600.-
Harold: Learned in Batman #458 \(\?\) . Also Ace, learned - but probably didn't understand, considering he's an ordinary dog - in Batman #465.
- Nomoz: Learned in Sword of Azrael #3.
- Dr. Shondra Kinsolving: Learned in LotDK #61, but had a mental breakdown shortly afterwards.
- Jim Gordon: Admitted in LotDK #125 that he *might* have found out if he wanted to.
- Lois Lane: Evidently learned off-panel in or shortly after Superman (vol. 2) #168 and 'Tec #756; knowledge revealed in Batman #611.
- Sasha Bordeaux: Learned in 'Tec #756.
Part 2: Costumed allies and other superheroes
- Wildcat: *Probably* knows since he taught young Bruce Wayne. Hinted in JLA #28.
- Martian Manhunter: Learned at some point prior to JLA: Year One #11.
- Robin/Nightwing (Dick Grayson): Learned - as depicted in numerous flashbacks - before becoming Robin.
- Robin (Tim Drake): Learned in Batman #436.
- The Outsiders (Black Lightning, Geo-Force, Halo, Metamorpho und Katana): Learned in Batman & The Outsiders #13.
- Robin (Jason Todd): Learned - in current continuity - off-panel following the events of Batman #409.
- Harbinger (Lyla): Knowledge revealed in History of the DCU. Monitor probably also knew.
- Batgirl/Oracle (Barbara Gordon): Knowledge revealed in Killing Joke. Learned (pre-Crisis) in Batman Family #3, later "forgot" and then learned again as revealed in 'Tec #526.
- Superman: Learned/knowledge revealed in AoS #440.
- The Titans: Many of them (might) know since they know Dick's secret ID.
- Raven: Probably learned in DC Comics Presents #26.
- Speedy/Arsenal (Roy Harper): Knowledge revealed in Action Comics Weekly #613.
- Cyborg (Victor Stone): Knowledge revealed in NTT #61.
- Starfire: Knowledge reaveled in NTT (vol. 1) #26 and #33, among others.
- Wonder Girl/Troia (Donna Troy, deceased): Knowledge revealed in NTT (vol. 1) #29.
- Flash (Wally West, former Kid Flash), Changeling, and Raven: Knowledge revealed in NTT #55.
- Tempest/Aqualad (Garth), Jericho (deceased), Lilith/Omen (Lilith Jupiter, deceased), Phantasm, Bumblebee, Flamebird, Mal Duncan and Jesse Quick might also know. As probably do Titans enemies Baron Blood, H.I.V.E and Deathstroke (for the latter see below).
- Waverider: Knowledge revealed in Batman Annual #15. Matthew Ryder, Rip Hunter and Liri Lee might also know.
- Azrael (deceased): Learned in Sword of Azrael #3.
- (The Hood only knew "Sir Hemingford Gray" (see Shadow of the Bat #23), *not* Bruce Wayne.)
- Aquaman: Learned at some point prior to Justice League: A Midsummer's Nightmare #2.
- Deadman: Learned at some point prior to Batman #530.
- The Spectre: Jim Corrigan knew (see Batman #541), as does Hal Jordan (see JLA #35). The latter might have not yet known when he was GL and Parallax.
- The Phantom Stranger: Knowledge revealed in Batman/Phantom Stranger.
- Wonder Woman (Diana): Learned at some point prior to The Kingdom #2.
- Flash IV/Dark Flash (Walter West): Knowledge revealed in JLA #33.
- Green Lantern (Kyle Rayner) and Plastic Man: Learned in JLA #50.
- Green Arrow (Oliver Queen): *Might* know/have known as hinted in Green Arrow (vol. 3) #5.
- Batgirl (Cassandra Cain): Learned in Batgirl #24.
- Atom (Ray Palmer): Knowledge revealed in JLA #78.
Part 3: Personal enemies and other villains
- Thomas Woodley (deceased): Knowledge revealed in LotDK #5.
- The Appellaxians: Knowledge revealed in JLA: Year One #11.
- Joe Chill and the Reaper (Hudson Caspian; both deceased): Learned in 'Tec #578.
- (Dr. Hugo Strange: Learned in LotDK #11-15, but was finally "convinced" otherwise in Gotham Knights #11.)
- Ra's Al Ghul, Talia and Ubu: Knowledge revealed in Batman #232, Talia might have already lerned in 'Tec #411. Other of Ra's' henchmen know as well, including Whisper A'daire (see 'Tec #743).
- Deathstroke: Learned in NTT (vol. 1) #39, knowledge definitely confirmed in Deathstroke: The Terminator #8.
- The Manhunters: Intercepted Harbinger's transmission from The History of the DCU as revealed in Millennium #2.
- The Joker: Possible knowledge *hinted* in Batman #429.
- Tsunetomo (deceased): Knowledge revealed in 'Tec Annual #3.
- Carleton LeHah: Learned in Sword of Azrael #3.
- Killer Moth: Knew at one point but doesn't know anymore as hinted in Shadow of the Bat #8 (referring to an old story from 'Tec #173).
- The "Nobody" und Doc Creasay (both deceased): Learned in Shadow of the Bat #13.
- Bane and Bird: Learned in Batman #495. Trogg and Zombie might know as well.
- Deathwing: Believed he was Dick Grayson and probably knows/knew, as hinted in NTT #100.
- Benedict Asp and Fritz (both deceased): Learned in LotDK #61.
- Neron: Knowledge revealed in Underworld Unleashed #2.
- Dr. Patrick Kryder (deceased): Learned in Batman Chronicles #17.
- Prometheus: *Probably* learned in JLA #36.
- Sneaky Pete, Ruby and Ruby's brother (all three deceased): Learned in Batman #577.
- Owlman (Thomas Wayne): Learned in JLA: Earth 2.
- Lady Shiva: Knowledge revealed in Gotham Knights #8.
- David Cain: Knowledge revealed in Batman #605.
- Hush also seems to know, whever he/she is. Probably already on the list, though.
Feel free to correct me. \:\-\)
This was an old post. Feel free to cite more recent DC issues where characters learn Batman's secret identity (permanently or not)?