I've done a MS and PhD in mathematics/computer science field (used same software throughout)
Windows (XP or 7)
1) Firefox + adblock, noscript - Being able to safely mine the web for the specific thing I want is extremely important. (free)
2) Dropbox - syncing the laptop and desktop in a way that is not a hassle, and free (free)
3) LaTeX - I prefer TeXNicCenter, but whatever floats your boat. Latex is the absolute best means for creating professional documents/presentations (free)
4) Foxit Reader - free PDF reader, makes Adobe Acrobat look like a slug going uphill, also available is a free windows search plugin to allow windows to index PDF (free, or buy for more features)
4.1) CutePDF - print to PDF, makes getting things from the screen to a printer or colleague easier. (free)
5) Visual Studio Pro - Eclipse and Netbeans are nice, but for C++ on windows VS seems significantly more polished (though eclipse does have a few features VS does not) (free to students through dreamspark)
6) Linux - great for running simulations where you want to minimize the amount of junk running in the background (this is near impossible on windows), VI for quick edits is also a cakewalk (free)
7) R - beautiful graphs, plenty of built in stat function, and under constant development. The graphing alone is a good reason to use R (free)
8) Notepad++ - Excellent text editor, and through macros, you can cause it to behave like an IDE for many languages (python, R, perl, fortran, etc...) (free)
9) Force - Fortran IDE for windows. The IDE leaves much to be wanted, but when working with people not *nix friendly, it is the only free fortran IDE on windows. If you have money get Visual Fortran from PGI (free)
10) Matlab - Don't really like it, but it does make analyzing matrices easy ($100ish for students)
I also use Office 2007 but when it comes to a final draft of a paper or presentation - it will be in LaTeX,