First off, Jerome Agel's The Making of Kubrick's 2001 is excellent. It's the sort of making-of book they just don't do any more, with plenty of insight into the film-making process, rather than a simple slapped together collection of publicity stills. It's out of print now, but there are still copies floating around, so keep your eyes peeled for it in charity shops. (Big thanks to Michael for my copy!)
Taschen have done their usual trick of publishing one cheap and cheerful book, Kubrick, one amazing, reasonably priced book, The Stanley Kubrick Archives, and one overpriced lump of gimmicky naffosity that wastes genuinely interesting material, Stanley Kubrick's Napoleon: The Greatest Movie Never Made. That second one is one of my favourite books about anything, ever.
Unsurprisingly, the BFI are always good for film books, so James Naremore's On Kubrick, Michael Chion's Kubrick's Cinema Odyssey and Peter Kramer's 2001: A Space Odyssey: BFI Film Classic (a bit colon-heavey that one) are all worth a look. Chion has also written Eyes Wide Shut: BFI Film Classic, but I take exception at the entirely unjustified use of the C-word there. It's not a classic, it's merely an okay film that happened to be made by a genius.
(I should point out that whilst writing this, my iPhone has decided to start playing Chris Isaak's Baby Did a Bad Bad Thing, from Eyes Wide Shut. Creepy.)
Cinefex Magazine Issue 85 from April 2001, probably the best behind-the-sfx look at 2001 anywhere.
Norman Kagan's The Cinema of Stanley Kubrick and Vincent LoBrutto's Stanley Kubrick – both come highly recommended. There's also Drama and Shadows, a rather beautiful collection of work from Kubrick's life as a photographer in the forties.
For other Kubrick resources, you can do a lot worse than Coudal Partners' astonishing Kubrick linkdump, which could keep you busy for a week.