To input the following codes, go to the start menu, then hold down the L2 button, and enter the rest of the code.

BulletProof Crypto
Square, Circle, Left D-Pad, Left D-Pad, Circle, Square
Aware Like A Fox
Right, Square, R2, R1, Right, R2
Nobody Loves You
R2, Right, R2, R1, Square, Right
Ammo-A-Plenty
Left D-Pad, Circle, R2, Right D-Pad, R1, Square
Deep Thinker
R1, R2, Circle, Right D-pad, R2, Circle
More Upgrades
You need to input this one from on board the mothership. Square, Circle, Left, Left, Circle, Square (Same buttons for the "Bulletproof cheat but different effect)
Mmm Brains!
Like "more upgrades" this must be entered while on board the mothership. R1, R1, R2, R2, Left, Right, Left, Right, R2, R1