This is a tough call, because most reference works don't really mean anything until you understand what is going on with photography, and once you understand what is going on with photography you don't really need the reference works.
Understanding Exposure is a must-have, IMO. It is one I keep going back to.
The Freeman books that I have read, The Photographer's Eye and Mastering Color Digital Photography, are excellent, but in my opinion they are not very useful to a beginner. I couldn't say about his others, I haven't read them.
I have Kelby's Digital Photography, both volumes 1 and 2. I like them; his informal style fits with mine. Lots of people don't like his style, but I do. I also prefer his books on Lightroom and Photoshop to the more scholarly works. Kelby describes his manner to be as if he were standing there advising you on how to get a particular shot. You understand how to get the results, then work it backward to understand the theory. Results oriented is good for a beginner, I think.
Before I decided to really figure out this stuff, I got good compositional ideas from Digital Travel Photography Digital Field Guide. Better vacation photos are always good.
Above all, I would have to say that the $100 I spent on the online course at Proud Photography was better than any $100 worth of books I've bought. (I don't get anything for saying that.) The course is untimed, you can progress as you like (I had a 3 month lapse between lessons at one point). The lessons are easy to understand and complete, and the feedback is constructive, timely and useful. Books are great, but there is nothing like having a professional look at your work and tell you what to do to make it better, telling you what you did right and what you did wrong.
Just my .02