In general I try to use community supported freeware, such as using R for all data management, analysis, and graphics. All graphs for this blog were generated using the ggplot2 package in R, which is a powerful and flexible graphical package developed by Hadley Wickham. I also use and recommend the RStudio integrated development environment for R. All statistical analyses were conducted using R base stats functions, or various packages as detailed on each post. Final graphics production happens in GIMP 2, which is a free and open source image editor. And of course, Microsoft Office products are used for various bits and bobs.
For those of you who might be new to data analysis and visualization, or who simply want to learn how to use R, I highly recommend swirl.
Data on the Rocks 