I believe a reference manager like jabRef would help you,
jabref is available from the repositories.

jabRef uses the Bibtex standard to store information about a wide variety of document types the Bibtex file is an ascii file that looks like this:

@article{Gettys90,

   author = {Jim Gettys and Phil Karlton and Scott McGregor},

   title = {The {X} Window System, Version 11},

   journal = {Software Practice and Experience},

   volume = {20},

   number = {S2},

   year = {1990},

   abstract = {A technical overview of the X11 functionality.  This is an update

of the X10 TOG paper by Scheifler & Gettys.}

}

Your documents does not have to be books and they can be hard copies on a shelf or in a filing cabinet, or electronic on your computer, in the case of physical documents you just number the articles and use that as the number in the BibTex file, if they are electronic you can have a link to them in the BibTex file, they could even be on the internet.

You can read more about BibTeX here:

http://en.wikipedia.org/wiki/BibTeX

Take a look at the various Entry types. When you use this method to manage papers you have great flexibility as jabRef can export to many other Reference formats or export your library to a web page and so on. jabRef also has a good search facility. you can create citations for Latex and Office documents that refers to your papers.

jabRef tutorials are here:

http://www.cs.rpi.edu/~tayloj/JABREF.TUTORIAL/

There is a warning about this being old but from what I see it is still applicable.

http://www.youtube.com/watch?v=QRteWsNfMeg

This YouTube video is also helpful.