A few days ago, I decided it was time for my assorted bibtex files to grow up and get organized. I also decided that my assorted pdfs of papers should also get centralized and organized. I had the crazy idea, that there might be a tool that could do both of these tasks in an open, portable format that I could easily transition if I grew tired of the tool. Unlike past endeavors, in this task I succeeded beyond all expectation. The JabRef reference manager is an open source reference manager that uses the standard bibtex format as a backend. Unlike other tools I tried, it works, simple and pretty feature-complete, it provides a centralized location to store references, notes/review/summaries of said references, as well as links to the actual pdfs (when you have them). JabRef will automatically generate bibtex keys for you, if you ask it, and if you save your pdfs with the respective key in its filename, JabRef can automatically find the file and associate it with the intended reference! Plus, like many of the other tools, it can automatically sync up to many of the online databases and download documents if you have access to them.
It also has extremely flexible keyword/category-based organization of references. Your categories can inherit either supercategories, subcategories, or neither.
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