To easily defeat the last boss (Alien Queen), equip the flamethrower and then get down on your stomach and constantly fire at her. As long as you are crawling on your stomach, she can't hurt you.
Get All Items
Pause game, highlight help text, hold L1+L2+R1+SQUARE, and then press X. You should hear a sound.
More Ammo
For more ammo, pause the game during normal gameplay and press Triangle. You should hear a sound if done correctly.
More Health and Armor
For more health and armor, pause the game and press triangle. Then highlight "HELP TEXT." Press and hold L1 + R2 then press X. You will hear a sound if done correctly.