You get these after getting a certain amount of skill points or doing other tasks.

Clank Backpacks: Get 100 skill points
Concept Art Pack 1: Get 10 skill points
Concept Art Pack 2: Get 20 skill points
Flip Levels: Get 70 skill points
Movie Player: Beat the game
MP Mechanic Skin: Get 126 skill points
MP Soldier Skin: Beat the game on superhuman
The Mighty Wrench (allies Get a wrench): Get 40 skill points