Is there any smart way to manage scientific papers for offline use in a linux system.

For example:

• It should be possible to tag papers with customizable tags, sort them by tags and so on
• if I see a new paper on arxiv.org and want to read it if I have more time, there should be a nice way to put it to my "read it later list" of my paper manager
• the paper manager should allow me to store bibtex data
• it should give an easy way to write down notes and comments to individual papers (supporting math-formulas)
• support pdf and djvu
• should be easy to backup

I don't need any integration to word-processing software.