Collecting a total of 30 data fragments unlocked narrow doors in the Black Room, allowing Desmond to witness several vital moments of his life. These could also be unlocked via the system update.
Collecting a total of 50 data fragments unlocked the locations for the remaining 50 on the Animus minimap.
The achievement "Capped" could be earned by collecting all Animus data fragments.
Assassin's Creed: Rogue
Collecting the fragments unlocked a message from Juno.