I have tried eLibPro (
http://songstech.com/elibpro.html) that worked pretty well on hard copy books. It allows links to the electronic version as part of the book info.
As far as organizing my eBooks, so far it is purely by author (A\Last, First - Title.ext), but I am always on the lookout for something better.
Now, for finding copies of files, there are programs such as mmd dupefinder (
http://www.mmdfactory.com/dupfinder.html), but it is apparently not checking MD5 sums, as some of the hits are definitely not duplicates. If someone knows of a better program, pass it along as well.