Paper organization
First of all, especially if you’re just starting out, tools to help you organize your papers are invaluable. Use one! They can help you keep track of what you read and keep your papers and notes together in one place.

• Mendeley Desktop – (Cross platform) I have a feeling this startup is going to make a huge impact on the academic world. I’m not too excited about the social networking aspects of their product, but the desktop application for organizing your paper collection is awesome. I also like how their developers are extremely interactive. I complained about a missing feature on twitter and the developer sent me an email with a fix within a day!
• Papers – (Mac only) This is a great program for organizing papers. If you have a Mac, download this and check it out. Personally I don’t use it, but that’s just because I don’t use Mac OSX.
• gPapers – (Linux, Windows) This is essentially a clone of Papers. I like it because it’s open source (easy to change) and it’s pretty nice. For a while I played around with it, but I ended up using Mendeley.
• EndNote – (Windows, Mac) I hate this program. Thomson Reuters owns the Web of Science database that indexes almost every academic paper ever written. Yet, for some reason, they haven’t integrated that with EndNote. It has a lot of potential, but it’s clunky to use and annoying as hell. I only mention it because a lot of people use this to organize their papers. Feel free to try it, but I’d recommend against it.

Writing

• LaTeX – (Cross platform) seriously, use it! It is so much easier to use than Word and it produces absolutely beautiful documents. Plus, it’s a must if you are doing a lot of math equations.
• latex-makefile – A great makefile for LaTeX documents.
• Vim – I love vim. More useful for coding than writing documents, but I still use it.
• Gummi – (Linux only) LaTeX editor. I like this because it automatically updates the pdf preview as you type. Plus, it’s open source, being actively developed, and the developer encourages contributions.
• TeXworks – (Cross platform) LaTeX editor. It’s useful. Doesn’t do auto-complete.
• Texmaker – (Cross platform) LaTeX editor. Lots of features. Too many for me.

Presentations

• LaTeX Beamer Class – (Cross platform) This makes some beautiful presentations. It’s admittedly not as easy as a visual editor, but the resulting quality is worth it (especially if you have a lot of equations) .
• OpenOffice Impress – (Cross platform) Normally I very much dislike the OpenOffice products, but I think they did a pretty decent job with their “powerpoint clone.” I use it for quick, short presentations.
• Powerpoint – (Windows, Mac) almost everyone knows about Powerpoint. 2007 has a lot of nifty features that can make some pretty presentations, but I don’t really like that much.

Figures

• Inkscape (Cross platform) – my favorite program for diagrams, drawings, etc.
• xfig (Linux) – vector graphics software. I find it to be very slow to use, but apparently it’s very useful if you learn the keyboard shortcuts.
• PGF and TikZ – TeX macro package that makes very pretty LaTeX graphics. Steep learning curve.
• GLE (Cross platform) – I haven’t actually used this yet, but it was recommended to me by a friend.
• Matlab (Cross platform) – I use Matlab for making plots. I think they’re kind of ugly though.
• Gnuplot – I sometimes use gnuplot for making plots. I think they’re very ugly.
• Dia (Linux) – Sort of like Visio. I’m not a huge fan of it, but I do use it on occasion. It can export directly to svg/eps/pdf which Visio can not do. Although, apparently Visio can be manipulated through some plugins and post-processing save as an eps (plugin to save as pdf->ps->eps).
• Graphiz (Cross platform) – Graph visualization software. Makes pretty graphs.