I thought The Two Towers was the best of the three. Helms Deep was a really cool war, especially when Gandalf and the Rohirirm showed up at the end. Also, I watched one of the special features and it said how Helms Deep was the hardest part of the movie to film, it had Viggo, John and Orlando expressing how hard is was to act there too because it was so increadibly cool. I appreciate the hard work that went into it.
Plus, the Two Towers focused on Gimli, Aragorn and Legolas, which is always good.