For the latest information on tools for fMRI analysis, visit NITRC (http://www.nitrc.org/)
Comprehensive fMRI Data Analysis Packages
FSL - http://www.fmrib.ox.ac.uk/fsl/
SPM - http://www.fil.ion.ucl.ac.uk/spm/
AFNI - http://afni.nimh.nih.gov/afni
Other useful packages for MRI analysis
Freesurfer - http://surfer.nmr.mgh.harvard.edu/
CARET - http://brainvis.wustl.edu/wiki/index.php/Caret:About
ANTS - http://picsl.upenn.edu/ANTS/
Tools for pattern classification analysis
PyMPVA - http://www.pymvpa.org/
Princeton MVPA toolbox - http://code.google.com/p/princeton-mvpa-toolbox/
scikit-learn - http://scikit-learn.sourceforge.net/