Bulletproof Crypto (invincibility)
Pause the game while playing as Crypto, then hold L2 and press Square, Circle, Left(2), Circle, Square. If you entered the code correctly, a message will appear.

Ammo-A-Plenty (infinite ammunition)
Pause the game, then hold L2 and press Left, Circle, R2, Right, R1, Square. If you entered the code correctly, a message will appear.

Deep Thinker (infinite concentration)
Pause the game, then hold L2 and press R1, R2, Circle, Right, R2, Circle. If you entered the code correctly, a message will appear. Your concentration meter must be above 0% or you will not be able to use any of your mental abilities. -From: evripple @ scubadiving.com

Pox Unlocks (all upgrades)
Pause the game while on the Mothership, then hold L2 and press Square, Circle, Left(2), Circle, Square. If you entered the code correctly, a message will appear. All upgrades for the currently unlocked weapons will be available for purchase from Pox's lab.

Mmm... Brains! (increase DNA)
At the Mothership's main menu, hold L2 and press R1(2), R2(2), Left, Right, Left, Right, R2, R1. If you entered the code correctly, a message will appear.

Aware Like A Fox (maximum alert meter)
Pause the game, then hold L2 and press Right, Square, R2, R1, Right, R2. If you entered the code correctly, a message will appear.

Nobody Loves You (reset alert meter)
Pause the game, then hold L2 and press R2, Right, R2, R1, Square, Right. If you entered the code correctly, a message will appear.