I have to agree with the feeling that has been building so far... The Sixth Sense. Absolutely, by far. It was a fantastic movie and its twist has become the prototype example for plot twist. It has made a huge and lasting impact.
The Sixth Sense was an all-around incredible film. Nothing else he's made even approaches it.
A big part of The Sixth Sense's near-perfection is its plot twist (which is not a gimmick or throwaway twist; the whole film is built around it), so once again, it has the best twist of all of his films.
The problem with the whole Shaymalan twist thing is that you go into the movie expecting one and then get to work trying to figure it out throughout the whole movie. This actually ruins the whole experience because you instantly get 3-4 theories together while watching which makes you miss the point behind the movie because you are looking for evidence the whole time. After that the movie can only be one of two things, something one claims they obviously saw coming the entire time, or something that was not good enough because theory #4 was better.
In this I think the 6th Sense was the only real big success because the audience did not go into it expecting a surprise at all. They just watched a film and was amazed at the end of what happened.