In order of merit:
1.Paths of Glory (1957) ****
2.Dr. Strangelove or: How I Learned to Stop Worrying and Love the Bomb (1964) ****
3.2001: A Space Odyssey (1968) ****
4.A Clockwork Orange (1971) ***1/2
5.The Killing (1956) ***1/2
6.Spartacus (1960) ***1/2
7.Barry Lyndon (1975) ***
8.Eyes Wide Shut (1999) ***
9.The Shining (1980) ***
10.Lolita (1962) ***
11.Full Metal Jacket (1987) ***
12.Killer's Kiss (1955) **1/2
The first 3 are practically interchangable but I've given the edge to PATHS due to its amazing performances and because it's one of the most scathing and moving indictments of war whereas, say, 2001 is more of a cold, perhaps even hollow technological exercise. STRANGELOVE, then, is my favorite among his films and, witnessing George C. Scott's jaw-dropping comedic turn always has me scratching my head as to why he didn't try that more often in subsequent years (although I know that Kubrick pulled that performance out of him through devious ways

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P.S. I don't know if it's actually true or not but I once read in an Italian film magazine that A CLOCKWORK ORANGE was Bunuel's favorite film. In that same magazine (which probably was a special Kubrick issue published after his death), Kubrick's favorite films were listed as well - and there were some surprising choices to be sure. I'll try to remember them and post them later on...