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My favorite is 2001. I've found that it's one of the only movies I've seen that makes me feel almost transcendent. It's his best, in my opinion. The reason most people found 2001 to be odd is because it's a boldly experimental film. It doesn't follow the traditional rules of narrative in cinema, it creates its own rules. There's never been anything like it. Apart from technical things like the effects and the use of classical music, the storytelling itself is unlike anything in history. I think that Kubrick wanted to show, not tell. Maybe the movie was filmed the way it was so that the audience can regard what's happening and think about everything. Most movies rush you to the next obligatory scene, abhoring things like mood and tone. This one doesn't. It allows the viewer to stand outside and consider questions that most other movies would give the answers to.
You can ask for explanations and look for meaning in every frame of the picture, but it's the way that the questions are raised that confuses most people.
That's just my opinion.
Also, Kubrick made some of the most beautifully photographed movies I've ever seen, ie Barry Lyndon, Paths of Glory, The Shining, Dr. Strangelove (still the most wicked satire I've ever seen), Eyes Wide Shut.
You ought to see Eyes Wide Shut. There's one scene in that flick that's sooo creepy. :::shudders just thinking about it:::
Why do you like Clockwork the best?