Free and Open Source Software That I Use
The R project for statistical computing
I use R for pretty much all of my statistical analysis and to prepare most figures. It's a bit difficult to use, I reccomend installing rStudio, which drastically improves the UI.
qGIS
As an alternative to ArcGIS, this is a powerful open source geographic information system.
ImageJ
ImageJ is a nice little image analysis application. I've used it for cell counts and sample measurements, but I'm just scratching the surface
GIMP
GIMP, or the "GNU Image Manipulation Program" is a powerful image manipulation application, comparable to photoshop
