Stanley Kubrick is certainly a high-achieving director. I find it difficult to choose my favourite Kubrick film because they really do switch genres so much. I haven't seen his first two films (which I heard weren't great) and never watched Spartacus (which he only directed). I've seen 2001: A Space Odyssey, A Clockwork Orange, and The Shining a few times at this point. I've only seen Paths of Glory and Dr. Strangelove once each and Barry Lyndon, Full Metal Jacket, and Eyes Wide Shut twice each. I'd have to give them a few more watches.
What really makes his films for me, though, are his themes. I can't speak much for the ones I've only seen once or twice, but certainly The Shining with its child abuse (both physical and sexual) subtext, gold-reserve-abandonment, and showing the Native American genocide; A Clockwork Orange depicting a new-coming of the Third Reich through pleasure and a government which claims to be against it (Kubrick was Jewish after all); and 2001: A Space Odyssey indicating the space race as maybe not all it seems, plus these themes repeating themselves through most of his films and even smaller themes within each movie, they really are communicated in an entertaining way that isn't too overt and makes you think they're preaching to the choir. I don't necessarily agree with all his themes, but he certainly presents them in an interesting way.
>My personal favorites, however, are Barry Lyndon and Eyes Wide Shut
Definitely enjoyed Eyes Wide Shut, though more so the second time around. It definitely doesn't hold your hand and Kubrick's use of "dream sequences" without telling you when the dream starts makes things very convoluted. Barry Lyndon was certainly filmed beautifully, but I can't say it's my favourite. I appreciate showing that having money doesn't necessarily bring you happiness. I'd rewatch it again, though, so clearly it isn't bad.