User peterstarts on Youtube has answered this and provided timestamps for the video clip below.
00:07 - Sallie Gardner at a Gallop
00:08 - Cat Trotting, Changing to a Gallop
00:09 - The Arrival of a Train at La Ciotat
00:10 - Annie Oakley
00:10 - Birth of the Pearl (right after the gun shot in Annie Oakley)
00:11 - A Trip to the Moon
Ali Baba and the Forty Thieves
The Great Train Robbery
00:12 - Little Nemo
Intolerance: Love’s Struggle Throughout the Ages
00:13 - The Champion
The Vampires or, The Arch Criminals of Paris
Joan the Woman
00:14 - Within Our Gates
The Nightingale’s Voice
Ballet Mécanique
00:15 - The Jazz Singer (which is shown during a scene at a premiere in New York where Manny goes to find out).
Black and Tan
The Hollywood Revue of 1929 (another movie which is reference right after they started to make talking pictures).
00:16 - Piccadilly (Lady Fay Zhu was inspired in Anna May Wong).
00:16 - The Wizard of Oz
00:19 - Ivan the Terrible, Part II: The Boyars’ Plot
00:20 - Tarantella
00:21 - Love Letter
Pather Panchali
00:22 - Duck Amuck
00:22 - Cinerama (The Rollercoaster iconic scene that goes from regular format to wide-screen for the first time).
00:25 - Ben-Hur (Chariots Race)
00:26 - Un Chien Andalou
00:27 - Psycho (The Bath Scene)
Dreams That Money Can Buy
Un Chien Andalou (again)
00:28 - Meshes of the Afternoon (the eye scene)
The Passion of Joan of Arc
Vivre Sa Vie
00:29 -Lucia
N.Y.,N.Y. (Oranges Scene)
The Wagoner "Borom sarret" (Traffic Lights Scene)
00:30 - The Black Vampire
00:31 - 2001: A Space Odyssey
Persona
00:32 - Week-end (Fin de Cinema)
00:33 - Matrix (1981)
00:37 - O-45
00:38 - Sunstone
00:44 - Raiders Of The Lost Ark
00:47 - Tron
00:49 - Terminator 2: Judgement Day
00:51 - Jurassic Park
00:53 - The Matrix
00:54 - Avatar
00:58 - Persona
02:21 - Singin' In The Rain (The End)