This is the MEG bible, with lots of information on all aspects of MEG measurements and analysis.
Look here for a slightly shorter Introduction to MEG by Cohen&Halgren.
For MNE-related papers, look at the corresponding MNE publication list.
Have a look at the Fieldtrip tutorials.
Look here for an Introduction to EEG/MEG analysis.
Look here for Recent CBU EEG/MEG Publications.
Look here for a tutorial of functional connectivity analysis.
You can find the books MEG: An Introduction to Methods, An Introduction to the Event-Related Potential Technique and Event-Related Potentials in the CBU library.