I honestly don't know how to pick. The problem with this question and this list of movies is that, aside from being directed by Kubrick, they really don't have much in common. They cover such a wide variety of styles and voices and tones that it's hard to compare. It'd be like asking who's better, Mozard, Miles Davis, or John Petrucci?
By that, how am I comparing them? Just which one I enjoy most? For me, that's also hard. I love a ton of them almost equally and films like FMJ and 2001 are just so completely different that I don't how to rate them other than #1 war film and #1 sci-fi film. You know?