Paine's library is documented in a manuscript "Catalogue of Books beloging to Robt. Treat Paine," with the Robert Treat Paine papers at MHS. Paine started his catalog in 1768, organizing the books by format (folio, quarto, octavo, &c.). He added to the list as he acquired new titles, and then reorganized the catalog in 1805, supplementing the organization with the addition of some "subject headings" (Law, Theology &c., History, Physiology & Philology, and Poetry & Belles Lettres).
An interesting feature of the library catalog is a list at the end of "books lent and to whom," revealing that Paine frequently loaned titles to various friends and relations (and almost always got them back, too). An interesting example is William Law's A serious call to a devout and holy life, which Paine loaned to "Miss Sally Cobb" (who would in 1770 become his wife) and to her mother, "Mrs. Cobb." Another is James Garton's Practical gardener, borrowed by General William Hull. The notes on loans are included with each applicable record.
On to the next! On deck is completing the catalog of Richard Cranch (the brother-in-law of John Adams, and a longtime friend of Robert Treat Paine, to whom Paine loaned a few books). Then it'll be on to David Cobb's library (Paine's brother-in-law) and Thomas Paine (his father). That is, unless some other library crops up and distracts me (as they are wont to do).
[Update: 25 July 2010 - I've added 156 more titles, after stumbling across a section of pamphlets from RTP's library in the 1850 book catalog of his grandson, Charles Cushing Paine].