FieldTrip is a Matlab toolbox for MEG/EEG analysis that is being developed by the F.C. Donders Centre in Nijmegen, the Netherlands. The toolbox includes algorithms for simple and complex analysis of MEG and EEG data, such as time-frequency analysis, sourceanalysis and non-parametric statistial testing. It contains high-level functions that you can use to construct your own analysis protocol in Matlab. It supports various file formats, and new formats can be added easily.
FieldTrip has its own website where you can download the code and documentation.