Batman is the main known case and I'm guessing it was obvious to him. The Batman Death Battle shows that he can remember even a face he's punched, let alone seen or palmed. Batgirl is even shown to recognize joker henchmen through facepaint, obviously a taught skill by Batman capitalizing on her eiditic memory. I've heard once Lex found out but chooses to ignore, or not believe that his nemesis works 9-5. I'll chalk that or ignorance up to his complete rejection of Superman being human, usually viewing him as an invader or alien or inhuman force that is the only match for his intellect. He plays by the same rule that Joker does in the New 52 Death of the Family arc. That being said the other genius character is Mr. Terrific, so does he know?
Beyond the "3 smartest men alive," who else has figured it out, if anyone? Have any humans been able to figure it out, not be told? Or have any heroes or villains prematurely greeted him as Clark rather than Superman?

Conduit found out and Perry White has hinted he knows but never admits it out loud, Manchester Black found out and Pre-Crisis Lois has found out several times.

I'm assuming you're refering to the New 52 timeline.

Up until now the only ones that figured it out by themselves were, Batman, Psycho Pirate, Ulysses and Constantine.

Lois suspected, but its clear she doesn't anymore. Lex never hinted that he knows. Wonder Woman knows because he told her, and the same applies to Cyborg, Aquaman, The Flash, and Hal Jordan.

And I'm guessing Darkseid also knows but he just doesn't care.

too many

The fact that is disguise is just a pair of glasses-not that many.

Lori Lemaris found out via telepathy.