Who Knows

 In: F.A.Q.

Who knew that Peter Parker was Spider-Man before the "Brand New Day" waving of the magical wand which made everybody forget.

Those Among The Living Who Know

Mary Jane Watson-Parker Since behind the scenes in Amazing Fantasy #15 as revealed in the Parallel Lives graphic novel, revealed she knew in Amazing Spider-Man #257.
Kaine Has Peter's memories
Eddie Brock
Since the second story in Amazing Annual #26, takes place between Spectacular #110 and Web #18, currently has amnesia
Felicia Hardy
Black Cat
Since Spectacular Spider-Man #87
Matt Murdock
Since Spectacular Spider-Man #107
James "Logan" Howlett
Since Spider-Man vs. Wolverine #1
Thor Since Marvel Team-Up #7
Warren Worthington III
Since Marvel Fanfare Vol. 1 #2
Thomas Fireheart
Since Amazing Spider-Man #273
The Watcher Sees Everything
Chief Examiner Since Questprobe #2
Nate Grey
Since Amazing Spider-Man #420
Judas Traveller  
The Gwen Clone Since Spectacular Spider-Man Annual #8
Dr. Strange
Stephen Strange
Since Marvel Team-Up Annual #5
Jessica Carridine Knew that Ben was Spider-Man
Kevin Plunder
Since Amazing Spider-Man #104
Jeannine Goodbe Kind of knows
Andrew "Paunch" Pauncholito Since Marvel Team-Up #130
Angelina Brancale
Since Amazing Spider-Man #397
Marandi "Mandi" Sjrokker
Since the "Hooky" graphic novel
Green Goblin I
Norman Osborn
Since Amazing Spider-Man #39
Doctor Octopus I
Otto Octavius
Since Amazing Spider-Man #397, currently has amnesia
Madam Web
Cassandra Webb
Since Amazing Spider-Man #210
Gaunt/Robot Master
Mendel Stromm
Currently has amnesia
Bounty Since Peter Parker: Spider-Man (Vol. 2) Annual 2000
Ezekiel Sims As revealed in Amazing Spider-Man vol. 2 #30
Charlie Clemmens As revealed in Tangled Web #7-#9
Aunt May
May Reilly Parker
Since Amazing Spider-Man (Vol. 2) #35
Kraven the Hunter II
Alyosha "Al" Kravinov
As revealed in Spider-Man: Get Kraven #1
Nick Fury As revealed in Spider-Man & Wolverine #1
Mr. Fantastic
Reed Richards
Found a camera with Spidey when he separated the symbiote in Amazing #258. Also, smart enough to figure it out any time he really wanted to. First actually shown to know in Daredevil (Vol. 2) #56.
Luke Cage First shown in Daredevil (Vol. 2) #56. Presumably learned at some time during New Avengers while he, Spider-Man and the rest of the team shared an apartment.

Those Among The Dead Who Know

Ben Reilly Has Peter's memories
The Kid Who Collects Spiderman
Tim Harrison
Since Amazing Spider-Man #248
The Burglar
Mr. Carridine
Since Amazing Spider-Man #200
Green Goblin III
Bart Hamilton
Dmitri Smerdyakov Kravinov
Since Spectacular Spider-Man #242
Seward Trainer  
Harry Osborn Since Amazing Spider-Man #135
Capt. George Stacy Since Amazing Annual 1996, takes place b/w Amazing #87 and #88
Scrier The original
Carrion I  
The Beyonder  
Tanya Anderssen Since Marvel Fanfare (Vol. 1) #2
Prof. Miles Warren
Spidercide/Freakface Has Peter's memories
The Robots of His Parents Since Amazing Spider-Man #387
Thousands of Spider-Clones Have Peter's memories
Aunt May actress/
genetic construct
From Amazing #400
The Stalker Since between Spectacular #263 and Spider-Man #98
The Thousand
Carl King
Since behind the scenes in Amazing Fantasy #15
Shathra, the Spider-Wasp
Sharon Keller
As revealed in Amazing Spider-Man (Vol. 2) #46

Those Who Might Know

Desiree Winthrop  
Joseph "Joe" "Robbie" Robertson Seems confused now
Other Scriers Probably were told
Debra Whitman Knows in her dreams
Norman Osborn Jr. Might have heard in Spectacular #200, although was very young
Phoenix III
Rachel Summers
Comes from alternate future where Spider-Man's I.D. was public knowledge
Carrion II
Malcolm McBride
Since Spectacular #149, though knowledge might have been lost when Carrion virus was purged from his body in ASM #393.
 In: F.A.Q.