Jubei Ninpucho (Ninja Scroll, 1993)
This is one of the best anime I've ever seen and easily one of the most brutal movies I've ever seen, but it handles the brutality in quite the fine fashion. Here's the link to my review, with more in-depth thoughts
http://worldsoforos.com/secondviews/2008/10/23/jubei-ninpucho-ninja-scroll-1993/
The African Queen (1951)
The effects leave something to be desired, and yes, it is a knock against the film. But, it's Bogart's best performance and Hepburn is well, Hepburn like usual. It's a simple story, but it works in spades. A man changing because of a woman and because of her innate desire to do what is right, but at the same time she must take stock of her life as he realizes how meaningless her earlier missionary work was and how wrong it was to try and "convert" the locals.
Who Framed Roger Rabbit (1988)
This belongs on the list just for the perfect job it did of blending animation with live action, as well as for the giddy mixing of Warner Brothers cartoon characters and Disney cartoon characters. The Daffy and Donald piano duet, dumbo outside the window, Bugs Bunny and Mickey Mouse on screen at the same time, so many awesome moments in that regard. But, when you look at the rest of the movie you realize how truly awesome a work it is. Not only doe it present the tremendous moral conundrum of what a toon is (for instance what is a sentient toon? Is Roger one, is the shoe that is dipped one, where is the demarcation line? etc.) but it is a classic film noir with some of the slickest dialogue put to screen as well as an award worthy performance from Bob Hoskins as Eddie Valiant. Easily in my top 20, a tremendous movie on every level.
American Splendor (2003)
First, Paul Giamatti is amazing in this, but so is Hope Davis and no one ever notices her. The weaving of reality and Hollywood is done so well and presents such a new and interesting take on the biopic. The subject material itself is tremendous, its both sad and hilarious at the same time. At the end of the day AS is Seinfeld, a movie about nothing that ends up being about everything as a result. But, unlike Seinfeld, you won't find caricatures in AS and everything is much, much darker, Splendid movie.