Citation databases that can be searched by topic and that has connections between sources, including journal articles and conference papers, that cite each other. It includes searches by cited reference as well as regular searches by keywords, title, and author.
Mendeley is a freemium tool to store references. It has a download for organizing and attaching pdfs and can be synchronized with a Web version for times when you are away from your computer. It has a recommendation system to suggest references based on the ones in your collection.