Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
i3 - A dynamic tiling window manager designed for X11, inspired by wmii, and written in C.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
dwm - dwm is a dynamic window manager for X. It manages windows in tiled, monocle and floating layouts. All of the layouts can be applied dynamically, optimising the environment for the application in use and the task performed.
Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.
Openbox - Openbox is a highly configurable, next generation window manager with extensive standards support.