The Super_Secret file is a .rar file located in the redist folder of Amnesia: The Dark Descent and is locked with a password only obtainable by getting all three endings of the game. After every ending, you will get a part of the password, and you must combine the letters and numbers in order to get the password.
The password is 7UI84S3D3AN2XJ36E7G5J26KA3Y9. If that doesn't work, use lke271tyr299odn314.
The .rar contains four folders, each containing unique content regarding the development of Amnesia: The Dark Descent.
Folder #1 - Video
This folder contains a couple of video footage that shows early production of the game.
"Very early level editor" footage
The video shows off a very early version of the level editor.
"Very early test" footage
The video shows off the HPL engine's capabilities.
"Early gameplay" footage
The video shows off some early gameplay mechanic demonstrations.
"Early alpha" footage
The video reveals some early levels in the game, and ideas and explanations regarding development.
Folder #2 - Art
This folder holds early concept art and similar stuff.
Creatures & Characters
This contains art regarding the many different areas and objects in Brennenburg Castle.
This contains a few paintings and drawings from around the castle.
Folder #3 - Design
This folder contains early game overviews and outlines.
One PowerPoint presentation
One .pdf detailing initial pre-alpha planning and overview from when the game was still known as Unknown.
One word document 
Contains maps, plans and descriptions of locations in the castle. 
This PDF contains information regarding the HPL engine.
Contains three sketches for the the editor.
A word document
This PDF details the initial idea and design regarding the engine.
Folder #4 - Herbert's Lost Diary
- The password (lke271tyr299odn314) is a possible reference to some of the old Nordic gods - Loki (lke), Tyr (tyr), and Odin (odn).
- 271, 299 and 314 are possible references to the mathematical constants e (Euler's Number), c (speed of light), and π (pi).
- In the Polish version of the game, one of the sound recordings from Herbert's diary is corrupted and will play noise. [Can we get a file upload of a recording of this Polish version-specific corruption?]