Essential Applications for Phd students

The ones that got me through my PhD were:

- LyX (http://www.lyx.org) for my thesis/conference papers etc. It's the greatest tool available for preparing any document longer than six pages and that needs to look good.

- Gnuplot for preparing figures and charts (gnuplot on its own isn't that pleasant to use, but gnuplotme is a script that makes life must easier (http://www.jamjoom.net/tools/gnuplotme/gnuplotme.html)).

- BibTeX for references (although Zotero is more current and excellent for collecting references online - it's a Firefox plugin and exports BibTeX if you want it to). I can also vouch for Mendeley as mentioned by another commenter, although I've only used it briefly.

- JabRef for managing my BibTeX database.

- Source code control! I wasn't as organised as I should have been with this and regret the amount of time it wasted me. Set up an svn/git repository as soon as you start developing any code, and use it!

- A good text editor: I know I'd be loath to suggest one on here so that's all I'll say on the topic :-)

- Dropbox wasn't around when I did my PhD, but it would be a must-have tool for a grad student. Backup your work!

- Powerpoint/Impress/Keynote. Don't get seduced by the LaTeX Beamer templates. They will get you geek cred but that's the only benefit.

- A calendar/organiser: Not that I ever got organised enough to use one, but if you want to finish within four years then it'd pay to get yourself organised.