Unlockable: Unlimited Eagle Vision

After beating the game, you can use Eagle Vision inside the Animus at any time, regardless of your health level (Synchronization).
Unlockable: Killing Without Penalty

After beating the game, you can kill anyone inside the Animus at any time, without losing health (Synchronization).
Migetsquasher
Hint: Accessing the Conference Room

After the credits roll at the end of the game you'll get an access code for the computer attached to the Animus. Once you hack the computer, you'll see an inbox, outbox and deleted message. Look at the inbox and choose the entry regarding the conference room. Now you can go to the conference room and access it via the keypad.
Maruraeko
Hint: Vidic's Access Pen

Before starting Memory Block 3, walk up behind Dr. Vidic and press any button to steal his pen. This will grant you access to his computer and emails.

Correction by Hayt03
Geychina
Easter Egg: Puzzle in Animus Room

After beating the game, go to the Animus room entrance door and activate Eagle Vision. Read the puzzle from right bottom to the left...