This is just a list of software I use and prefer, with links to it's official pages. I do cherish the idea of open source and free software, and I support free knowledge.
I use Debian as operating system:
http://www.debian.org
For my projects I usually prefer to program in C++ with Qt:
http://qt.digia.com/product
The IDE which I use for Qt development is QtCreator (I use it for non-qt projects as well):
http://qt-project.org/wiki/Category:Tools::QtCreator
I create documents with LaTeX, and use Kile as environment for that:
http://kile.sourceforge.net
For plotting I use gnuplot:
http://www.gnuplot.info
I use Meld to compare text files and directories:
http://http://meldmerge.org
To browse the internet I prefer Google Chrome:
http://www.google.com/chrome
Formulas and math expressions are written in LaTeX and are available troughout the blog thanks to a TeX online editor, courtesy of codecogs:
http://www.codecogs.com/latex/eqneditor.php
Source code snippets repository is provided graciously by codepad:
http://codepad.org
There are some other tools I use, but rarely, and I won't mention them here for now.