I currently use Mendeley (www.mendeley.com) to keep track of the papers that I have read, comment on them, and organize my references for my publications.
I know that papers is awesome - but I do a lot of my work from my Uni workstation which is a Linux box so papers isn't an option for me. Mendeley can be used and is synchronized across mac/pc/linux which means I can work/read anywhere.
It is possible to import new libraries from a .bib file. Unless that .bib file has some keys in it that point to the corresponding .pdf then you will have to link the pdfs to the library entries manually.
I have had a little success with importing pdfs directly, but the importer is very sensitive to the format of the pdf and the journal. eg, pdfs that are just images of the pages are not useful.
If you can export the file locations from bibdesk or from papers along with all the other meta-data that is in the .bib files then you won't have any troubles.
Excellent! Yup Papers includes the local-url tag so Mendeley imported all the PDFs to go with the papers. It did struggle a little bit with the older image-PDFs but loaded in the end. And it even kept the citation keys, something which Papers II continues to fail at (!). Not sure if I'll completely switch to Mendeley yet but it's definitely nice to be able to sync my library with Linux/Windows compatible software if necessary. Thanks again!