[Free] Mendeley makes it easy to keep your collection of PDFs organized. It takes PDFs, extracts author/title/source information, renames and organizes them, and syncs them to free online storage space. 2 GB limit on free version, with more available in premium versions. It also includes a PDF reader that allows highlighting and annotations.

Tutorials on some of the basic features in Mendeley.

An overview of the different uses for Mendeley.