The obvious one is three seconds. Another is the 10 second free throw violation. Also hitting the net while the ball is on its way through the basket. But these don't go completely unnoticed, and I will make the call if the situation actually warrants it. So not really ignored, just very leniently enforced
As for fouls, those I don't ignore. However, the determination of advantage/disadvantage can vary widely between age levels, skill levels, or even from game to game or from one part of a game to another. I know that last phrase sounds like I'm promoting inconsistency, but sometimes an otherwise decent game begins to tank and you have to tighten up to keep it under control, or there are times where you have to go get a "game control foul" that you normally wouldn't call.