In no real order here are my top 5 overlooked flicks
(1999) Boondock Saints - rather gory, but quite provocative.
(2001) Donnie Darko - big cult following, really explores the human mind, and especially teenage angst. Then throw in some of the other insanity, and it comes together as a great movie.
(2002)Equilibrium - Great movie, interesting view of the future, wonderful fight scenes.
(1997) Princess Mononoke - Great movie, albeit animated. Explores the conflict between the natural and industrialization. Weird ending, but interesting all the same.
(2000, 2003)Sci-fi Presentation of Dune and Children of Dune - One of the greatest adaptations from a book. Though both are close to six hours long, the story is developed well. Dune is done better that Chilldren of Dune, however Children is actually a combination of Dune Messiah and Children of Dune.