MEG papers
This is the [http://rmp.aps.org/abstract/RMP/v65/i2/p413_1 MEG bible], with lots of information on all aspects of MEG measurements and analysis:
Magnetoencephalography: theory, instrumentation, and applications to noninvasive studies of the working human brain Matti Hämäläinen, Riitta Hari, Risto J. Ilmoniemi, Jukka Knuutila, and Olli V. Lounasmaa Rev. Mod. Phys. 1993, vol 65, 413:497
For MNE-related papers, look at the corresponding [http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/MNE_register/MNE_Reading.html MNE publication list].
For SPM-related papers, you'll find links on our [http://imaging.mrc-cbu.cam.ac.uk/meg/SpmAnalysis SPM analysis page], or on the [http://www.fil.ion.ucl.ac.uk/spm/doc/ FIL pages].
Look here for an [http://www.mrc-cbu.cam.ac.uk:8080/research/eeg/eeg_intro.html Introduction to EEG/MEG analysis].