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I spent several years as a clearance consultant, having cut my teeth as the producer's assistant on Pollock, where I ended up handling most of the art clearances. The stories I could tell you (off the record, and only if I really trust you)...

A friend of mine emailed me today on just this topic, and I thought I'd share my response.

My friend from the dog park is in the process of editing his short (under 15 minutes) film, which he plans to enter in various festivals. The movie takes place in a bookstore and centers around a book of paintings. He is not sure about what type of permissions he needs to get to use the book in the film, I told him you may know, so I thought I would ask.

There are 3 levels of permissions involved here.

1) The paintings themselves. If the artist is a 20th Century+ painter, it is likely that his/her works are not yet in the public domain and the rights are controlled by the artist or their estate. Most artists are represented by Artists Right Society or by VAGA.
Both organizations have websites that list their clients. He will need to obtain permission that might involve a fee, though he should specify that this is a short film and he wants festival rights only. ARS and VAGA are both very easy to deal with, but they cannot guarantee that the artist or the estate will grant permission or be reasonable, and they don't negotiate.
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2) The book itself. He will need to contact the publisher and obtain permission to feature pages from the book in his film, as this falls under copyright protection. These rights will be much easier to obtain if he gets the artist's permission first.

3) The images of the paintings. When dealing with the publisher, the rights he asks for should specify the images on the pages, mentioning the specific paintings by name. If the publisher cannot grant this permission, he will have to go directly to museums or galleries who own the works. The publisher may demand this permission before
signing a release for the book.

And a second query:

The other question is does he need to get permissions for any of the other books that show up on screen? Some of the scenes are in front of bookcases clearly showing the spines of hundreds of books.

As long as none of the books are featured in closeup or singled out as featured props, you do not need to get permission. A shelf full of books where are all receive equal positioning constitutes fair use. Even if they are behind someone in a medium close up, you are probably fine as long as there are a bunch of books showing.

(Please note that I am not a lawyer, and you should make sure to consult with your own counsel for any clearance-related issues).