Enemies know where you are regardless of what happened. They could find you if you were in a collapsed cave 500,000 feet underground.
You can't wear the extra-protective armor that your enemies wear (Most, if not all FPSs).
Regenerating health.
Guns are less powerful than a slightly bigger than normal wolf (Final Fantasies and other RPGs)
Scaled enemies.
If there is a resurrection item in game, you cannot use it if a character gets killed off (RPGs)
The ultimate weapon in any case scenario either needs a ridiculously short/long amount of time to "charge up".
The good guy will lose in the beginning of a battle with a big baddy, but by the Grace of God, the enemy will reveal a weakness in their indestructability (RE bosses, rail shooter bosses).
The first evil guy you see is actually a puppet of an even more bad-ass antagonist.
Mobs of enemies have no group tactics (i.e stand by explosive crates/barrels/whatever), this happens less with the advancement of A.I.
There's always a "greater good" that you have to do.
Sidekicks always die or disappear when you need them. Same thing, really.
Vehicle sections/underwater sections.
That's all I got for now.