There are lots of ways of storing paper citations (you could even -shock horror- use paper) - the most established format is called BibTex. Essentially this is a database store of paper citations.

JabRef is a free and Open Source tool for storing papers (using BibTex). Since it is free you can easily download it and have a go. Download it from the JabRef home page

The rest of this page gives some help on using JabRef:

Install and run the program... It doesn’t do much until you import some papers - to do this you just need to save the paper citations to BibTex (or other compatible format) and import/open them:

1. In the paper database choose ‘Save As’
2. Choose a format (ideally BibTex - which is saved as .bib, but RIS and some others will work)
3. Save the file to your computer
4. In JabRef choose: File→Import (or Import and Append) → AutoDetect
5. Find your downloaded file and import, job done (hopefully).

If this doesn’t work, look at the JabRefImportList for more help.

1. Make sure that Options→PDF directory is pointing to your directory with papers in.
2. Click the ‘wand’ in the details view to generate the Bbtex key (a unique reference to the paper)
3. Name the pdf the key name
4. In the general tab, click ‘Auto’ – it should find the pdf.

To do this you need to ensure that the articles have a unique BibTex key and an Author, the import will throw an exception otherwise.

To import to CiteULike from JabRef:

1. Press Ctrl+G
2. Save your database
3. Go to CiteULike, Logon
4. Click ‘Import from BibTex’ (bottom left of screen)
5. Choose the file you have just saved
6. Choose some relevant tags.
7. Click Import

Job Done. Note – at the moment the article keywords are imported into CiteULike as tags. This kind of bodges up the tags, since keywords are generally vague and useless. To resurrect this, you currently have to go into each article and delete the tags/add appropriate ones. THIS IS IMPORTANT to maintain the integrity/usefulness of the tags in CiteULike.

CiteULike has an export to BibTex option - at the moment, this only exports your whole library, but hopefully this will change in the future.

1. Go to CiteULike and logon
2. Click the ‘Export to BibTex/EndNote’ option (under the ‘Your Library’ menu).
3. Choose the ‘Eport your library as BibTex’ option
4. Save the file onto your computer
5. You can either just open the .bib file using JabRef, or import it using the instructions above.

— Simon Judge 2006/01/16