RedCube is a great software application that allows you to sort all of the research papers that you have. You can manage, search, and sort all PDFs by folders. You can read them, take notes, and add annotations. The software also gives you recommended articles based on things that you read. It is definitely useful and a great tool for saving time when archiving and trying to locate old papers.
VUE is definitely a good recommendation for research paper needs. It is also open source and offers you the ability to organize your research in a visual way by using a mind map. You can add files, URLs, images, text and quotes into your mind map. This allows you to organize and tag your thoughts on your reading and research in a very effective way. It is similar to DocEar, but a bit easier to master.