Evernote is a versatile free tool which allows you to take notes, collect information in the form of documents, images and PDFs and store them in a single location. It is compatible with your smart phones as well as your computer. So, now you can work either from your smart phone on the way home and can continue working on your computer as the documents will automatically sync. It also allows you to add tags and keywords to the document so that they can be arranged in a particular order.
Evernote: Your online thumbnail.
Diigolet is a researching tool which will allow you to highlight text on webpages with different colors, add sticky notes, bookmark website or share text with friends. This application after installation becomes a part of your toolbar and all your annotated links are saved in its library. This tool is available in both free and paid version.
DIigolet: Your personal online library.
Scrivener is a word processing and project management tool for authors. It is a paid service with a 30 day trial period. It allows you to create sections of your academic paper and arrange them later as per the format and flow of your paper. It also assists in researching and collecting data by allowing you to take notes. After the research is complete, it assists you to build the final paper by using proper formatting including footnotes and creating PDFs, Word, HTML and RTF documents.
Scrivener: your personal writter