Pause the game, then hold L and press White, Black, R, Left, X, Black, White.
Bulletproof Crypto (invincibility)
Pause the game, then hold L and press X, Y, Left(2), Y, X when you are Crypto.
Deep Thinker (infinite concentration)
Pause the game, then hold L and press Black, White, Y, Right, White, Y. Your concentration meter must be above 0% or you will not be able to use any of your mental abilities.
Pause the game while on the Mothership, then hold L and press Black(2), White(2), L, R, L, R, White, Black.
Alien From Ipanema mode
Pause the game, then hold L and press Y, Black, L(2), White.
Ammo-A-Plenty (infinite ammunition)
Pause the game, then hold L and press Left, Y, White, Right, Black, X.
Aware Like A Fox (full awareness)
Pause the game, then hold L and press R, X, White, Black, R, White.
Better DNA value
Every chance you get, do not kill a human before you extract their brain stem. Extract their brain stem first as it will make the DNA worth more (25 instead of 10). The easiest humans to do this to are the scientists in the level with glowing cows. For some reason, if the person that is important to you dies (the person you need to abduct), extract their brain stem before you return to the Mothership -- the DNA is usually worth more. Additionally, it is rare to find humans with brain stems that are worth 50 or 100 DNA. Most humans have brain stems that are only worth 10 or 25 DNA. If you walk around Union Town, there will be humans with signs on them reading, "REPENT THE END IS NEAR". Those humans will have a brain stem worth 50 DNA. Also, Mystery Agents' brain stems are worth 25 DNA points most of the time, whether dead or not.
Faster Destruction in the UFO
Instead of holding R to destroy buildings or large objects, tap R and the destruction will happen faster without waiting for the recharge.
Finding more probes
Probes are necessary to get upgrades quicker. In order to find them all, make sure to look high up on rocks or hard to reach places. Your jetpack is essential in getting to the high places. You may have to get up on the ledge or building, then use your jetpack to fly higher to get the probe.
Getting away from the law
Don't bother trying to run away from the authorities with short legs; use your jetpack liberally to fly away. Press Left Analog-stick Forward and hold A to boost away.
Pause the game, then hold L and press Black, White, Black, X, Black, White(2).
Put your target (dot in the middle of the screen) on any human, and press B. In order to maintain your HoloBob, you must read the thoughts of the humans walking around. You can read the same person's thoughts repeatedly to keep your mental powers charged.
I Told You I Was Hardcore mode
Pause the game, then hold L and press White(2), R, X, Y, Black, White, Black.
It you levitate a person for a long time, they will die.
Lower brain juice meter
When you are in the form of another person, to make you brain juice meter go down, read other people's thoughts.
Monkey Brad (annoys FlexMentallo)
Pause the game, then hold L and press White, R, Left, Black, Y, White, Black, X.
Stand in an open area on any level and walk forward. Keep decreasing your speed until you eventually begin walking in place.
Collect all the probes in the indicated side mission to unlock the corresponding movie in the Furonigami option under the Archives menu:
Art Of The Furon movie: Santa Modesta side mission
Blue Book : Saucer Blueprints movie: Rockwell side mission
Evolution Of An Alien movie: Turnipseed Farm side mission
Nobody Loves You (no awareness)
Pause the game, then hold L and press White, R, White, Black, X, R.
Plan 9 From Outer Space reference
Halfway through the game you will experience a level where you go to the drive-in to switch films with the one that is showing. Watch what is showing before you switch films to see that the film is Edward D. Wood, Jr.'s Plan 9 From Outer Space.
Allow the game to idle at the mission selection screen and Pox will make various remarks.
Pox Unlocks (all upgrades)
Pause the game while on the Mothership, then hold L and press X, Y, Left(2), Y, X. All upgrades for the currently unlocked weapons will be available for purchase from Pox's lab.
Allow the game to idle for awhile; eventually the screen will turn black and white and elevator music will play in the background.
After getting out of your UFO, aim at a human and press Y. When you have changed into the human, the bar on the top left corner of the screen will go down. When it is all gone, you will change back into an alien. If you want to remain human, turn into a human and while walking around, scan other humans or animals to make the bar on the top left corner stay up.