There are a few ways you can organize the digital papers you download.
1. One such way is using Zotero. Basically, Zotero [zoh-TAIR-oh] is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources.
2. Another one is to use Mendeley.
In addition to being multi-platform, it also has
a web site where you can sync your PDFs for online access. It also extracts the metadata from your PDFs (like title,
authors, journal titles) and fills in many fields for you. You also have PDF renaming options.
3. Finally, a lot of people use papers: http://mekentosj.com/papers/
I haven’t tried any of these though, so I wouldn’t know which one to recommend. I personally just organize the PDF’s by fields of research and name each one as the title of the paper. It helps having hard copies as well 😀