This is a difficult choice for me.
I love Batman Begins. I think the story is amazing, the pacing is really great, the characters are friggin' awesome...... and Scarecrow is a pretty menacing villain. However, the first half of the film is (understandably) slow, and Scarecrow gets very little screen-time, thus, it feels like the movie did not do him justice. I love it, but it is probably my least favorite of the three.
The Dark Knight is generally considered the best of the three. The characters, the story, the pacing, the soundtrack, the action, the plot, the acting, it's all there....and The Joker is one of the best portrayed villains ever, probably. The slowness that the first film had is not present here, and the villain is done justice. Overall, exceptional film.
The Dark Knight Rises is probably considered by most to be (not the worst), but the least-good of the three. The film puts a greater focus on the minds of the characters, and shows Bruce Waynes struggle to find his true self: Bruce Wayne, or Batman? The acting and dialogue are still very good, the action and effects are the best of the trilogy, and soundtrack is still epic, the pacing is exceptional, and Bane is the most badass and menacing villain of the trilogy. The sense of urgency and severity is so prevalent, and perhaps best of all, the movie does not rush itself: it takes it's time. Now, there are some pretty noticeable plot-holes that make the plot a bit unstable, but overall is a very enjoyable film.
So, Batman Begins is my least favorite, and I have pretty much balanced the pros and cons of The Dark Knight with the pros and cons of The Dark Knight Rises, so I am going to have to say that I vote it is a TIE between the latter two films. Both are equally exceptional. The first film is nearly as good, with just a few too many cons to hold it back. Overall, the entire trilogy is one big masterpiece.
Now....the opinions of others is important. So you should share yours.