Papers is a popular program that specializes in managing pdfs of scientific articles. Within Papers, search major scientific article databases, including PubMed, IEEE Xplore, and Web of Science. Papers will import the relevant metadata (author, journal title, etc.) for you. In the Reader window you can annotate your PDFs by highlighting or underling in different colors and adding notes.
A free 30-day trial is available from the Papers website for Mac or PC. Papers can be downloaded from the web for a fee, and students get a discount. A Papers application for the iPhone is also available.