(2)The space-time is a lot more flexible than physicists admit. Its flow is easily interrupted and cheated. Portals and time machines are common. Most evil government groups have at least one, and many have several. (Half Life, Quake I&II).
(3)All apparently empty rooms have hidden monster spawns. No exceptions. (Survival Games)
(4)Medical kits will cure everything from radiation poisoning to leukemia, to poisoning, to missing limbs and head wounds instantly, upon contact. (Every game)
(5)Most evil people and beings are fond of zombies. (Doom I,II,III, System Shock series, and more)
(6)Electricity prefers to shoot out in lightining bolts through the air rather than taking the shorter paths. (Half life, etc)
(7)If you shoot up, the bullet WILL NOT come down. (Any shooter game)
(8)Backwards recoil does not apply when aiming up or down. (Half Life)
(9)Rare earth elements are THE key component of research into alien life (System shock 2).
(10)Newton's laws don't apply in space. When engines die, you slow down, and you cannot accellerate beyond your top speed. Also, explosions are louder in a vacuum. (Space combat games)
(11)Protagonists have special abilities that cause bullets to miss them automatically (applies to James Bond and Action movies too).
(12)There's no such thing as gravity in space. Once you stop, nothing will move you, no matter how close you are to a star or planet. (space combat games)