* Zotero - a Firefox-plugin that help me organize papers, citations, web-pages and other resources. All papers/notes are saved in "the cloud" for easy access across multiple terminals (...or Firefoxes). A great tool that enables you to tag, add notes, cross-link papers, add comments to/highlight text in PDFs, etc.
|The Zotero Firefox plugin.|
* Freemind - a mind-mapping tool. It was the best (open source) mind-mapping tool four years ago - and I believe it still is. Its written in java, so some slowness is included. It has great export functionality as shown in this HTML exported mind-map with the topic "FLOSS development".
|Freemind mind-mapping tool.|
* Dia - to create professional looking figures for use in papers.
* Dropbox - to sync all my resources (PDFs, papers, presentations, etc) across multiple computers. I might switch to Ubuntu ONE later - but Dropbox works, and it works well.
* OpenOffice (LibreOffice) Draw - to create PhD-posters. Read my howto here.
* I write all my papers in Emacs with the AUCTeX LaTex mode and RefTex to create the TOC speedbar (see screenshot below). For notes I use xpad, and all revision control is done in Subversion (papers, documents, figures, presentations, code).
The desktop manager is Fluxbox with a bunch of key-bindings, bfpager, and gkrellm with bfm-plugin for system monitoring (I like to watch my system resources). Its the same setup I've used for years:
|Screenshot of my current workspace: Fluxbox with gkrellm, Emacs, 2x xpads and 2x terminals.|