A gameplay mechanics is just as much IP as anything else. People have software patents/method patents on things like "minigame during loading screen"(Namco) and other such random items. Freecraft used mostly all origional art, but copied the gameplay(and namesake) of Warcraft close enough that it got shut down by blizzard.
Look at all the maps for LittleBigPlanet that get removed from the online download because they are replicating another game's gameplay using the LBP engine.

For the most part you can't copy any gameplay mechanic if you are presenting it in the same light as the origional. If the first company to make "QTEs to open a door" decided to go after people for it, and they had the forsight to get the right paperwork out of the way, then they'd be the only company using QTEs on door progression. Everyone else would be risking patent/trademark infringement. Thankfully that happens fairly rarely, and even when it does, publishers QA departments have legal counsel who will force the removal/change of offending gameplay or art.

Some things are too trivial, have prior art, or just aren't worth dealing with. There are tonnes of platformer games like Mario, no of which are Mario. There are tones of RTSs like Starcraft and C&C. And almost every FPS is the same game minus the setting. Other things like "the gravity gun" could easily be a point of contention as different art with a similar enough in feature set would instantly hit against the tradmarked image of HL2 and GordonFreeman. In exactly the same way TomSloper mentions you shouldn't use AK-47 as a gun in your game.