Mendeley is a research management tool for desktop & web. It has clients for Linux, Mac, Windows and iPhone and a Web interface. Mendeley can manage any documents, but is better to work with PDF. The file meta data are synchronized though Mendeley server. The attached files (PDF or any other formats) can also be synchronized, but the free account has a quota of 500MB. However, the attached files directory and underlying sqlite database can be synchronized manually.
This article demonstrates how to quickly switch to a window using gpicker and wmctrl. You type significant letters of workspace name, application name or title and gpicker provides a list of windows you most likely mean to pick.