So (for fairly obvious reasons) I decided to look through and see if I could compile a full list of everyone who knows Peter Parker's secret identity so far. Amazing Spider-Man (vol. 3) #1 distinctly shows who exactly knows at that point in time, so those are:
Mary Jane Watson
Mr. Fantastic
Invisible Woman
Human Torch
The Thing
Hawkeye
Mockingbird
Iron Fist
Spider-Woman
Captain Marvel
Wolverine
Jessica Jones
Luke Cage
The Winter Soldier
Doctor Strange
Kaine
Julia Carpenter
Jackal
Captain America
Carlie Cooper
Miles Morales
Anna Maria Marconi
Spider-Man 2099
And since then, these are the others who are revealed to know or find out.
Doctor Octopus
Anya/ Spider-Girl
Silk
Spider-Gwen (and the rest of the Web-Warriors)
Hobie/Prowler
Ben Reilly
spoilers:end of spoilers
Teresa Parker
and now J. Jonah Jameson
If there's any I'm missing, let me know.