Software

General

• Total Commander (free) - file manager
• WinSCP (free) - file transfer tool
• TeXnicCenter (free) - LateX editor
• Mendeley reference manager (free) - manage references & automatic bibliography generator for MSWord, LibreOffice and BibTeX
• SeaMonkey (free) - internet application suite including web editor
• Git (free) - version control software and Dmytro's tutorial

Imaging Analysis

• SPM (free) - general purpose (fMRI oriented)
• PDC (free) - partially directed coherence analysis
• FieldTrip (free) - general purpose (EEG/MEG oriented)
• Brainwave (free) and documentation - MEG analysis toolbox
• CARET (free) - anatomical reconstruction toolkit for structural and anatomical data (simple tutorial)
• Atlas for identifying brain regions / function based on fMRI meta-analyses

Machine Learning

• Kevin Murphy's Kalman filter toolbox (free)
• libSVM - Support Vector Machine Library
• Andrew Ng's ML Programming Exercises

Vector Graphics

• CorelDraw - ask Gunnar for installation CD
• Inkscape (free)

Statistics

• SPSS - general purpose
• R (free) - general purpose with great online book!
• psignifit (free) - psychometric function fitting