My favorites would be:
* Mark Levine: The jazz theory book
This one is great to understand general jazz theory. He doesn't allways get it right, but I still find it to be the most complete and comprehensive book on the subject.
* John Scofield: Time on my hands
Transcriptions of all the tunes from that album (one of the greatests albums ever in my book) with themes, guitar-solos, chords, tabs, everything
* Joe Pass: Jazz lines
This is actually an instructional video but it comes with a booklet / pdf. It's a collection of frases and etudes (major, minor, domininant, altered respectively). The booklet can easily be used without the video, but the video is also recommended because he talks a lot about how to simplify ones thinking besides actually playing all the frases and etudes.
* Bert Ligon: Connecting chords with linear harmony
Recently I've been checking out this book. It seems to be the best I've seen on the subject of jazz improvisation.
By the way I have yet to find a complete, comprehensive, systematic book on guitar chords voicings. I've been checking out several but most seem pretty messy in my opinion
