This list is far from complete, many more algorithms that have been published in papers are implemented in FieldTrip. If you want to know which paper describes a method in detail and it is not given here, you can ask on the email discussion list.
Cuffin BN, Cohen D. Magnetic fields of a dipole in special volume conductor shapes. IEEE Trans Biomed Eng. 1977 Jul;24(4):372-81.
Huang MX, Mosher JC, Leahy RM. A sensor-weighted overlapping-sphere head model and exhaustive head model comparison for MEG. Phys Med Biol. 1999 Feb;44(2):423-40.
Nolte G. The magnetic lead field theorem in the quasi-static approximation and its use for magnetoencephalography forward calculation in realistic volume conductors. Phys Med Biol. 2003 Nov 21;48(22):3637-52
R. Kavanagh, T. M. Darccey, D. Lehmann, and D. H. Fender. Evaluation of methods for three-dimensional localization of electric sources in the human brain. IEEE Trans Biomed Eng, 25:421-429, 1978.
Cuffin BN, Cohen D. Comparison of the magnetoencephalogram and electroencephalogram. Electroencephalogr Clin Neurophysiol. 1979 Aug;47(2):132-46.
Fuchs M, Kastner J, Wagner M, Hawes S, Ebersole J.S. A standardized boundary element method volume conductor model. Clin Neurophysiol. 2002 May;113(5):702-12.
Oostendorp T, van Oosterom A. The potential distribution generated by surface electrodes in inhomogeneous volume conductors of arbitrary shape. IEEE Trans Biomed Eng. 1991 May;38(5):409-17.
Van Veen BD, van Drongelen W, Yuchtman M, Suzuki A. Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Trans Biomed Eng. 1997 Sep;44(9):867-80.
Gross J, Kujala J, Hamalainen M, Timmermann L, Schnitzler A, Salmelin R. Dynamic imaging of coherent sources: Studying neural interactions in the human brain. Proc Natl Acad Sci USA. 2001 Jan 16;98(2):694-9.
Scherg M. Fundamentals of dipole source potential analysis. In: Auditory evoked magnetic fields and electric potentials. (eds. F. Grandori, M. Hoke and G.L. Romani). Advances in Audiology, vol. 6. Karger, Basel, pp 40-69, 1990.
Dale AM, Liu AK, Fischl B, Buckner RL, Belliveau JW, Lewine JD, Halgren E (2000): Dynamic statistical parametric mapping: combining fMRI and MEG to produce high-resolution spatiotemporal maps of cortical activity. Neuron 26:55-67.
Arthur K. Liu, Anders M. Dale, and John W. Belliveau (2002): Monte Carlo Simulation Studies of EEG and MEG Localization Accuracy. Human Brain Mapping 16:47-62.
Fa-Hsuan Lin, Thomas Witzel, Matti S. Hamalainen, Anders M. Dale, John W. Belliveau, and Steven M. Stufflebeam (2004): Spectral spatiotemporal imaging of cortical oscillations and interactions in the human brain. NeuroImage 23:582-595.
Mitra PP, Pesaran B. Analysis of dynamic brain imaging data. Biophys J. 1999 Feb;76(2):691-708.
Jarvis MR, Mitra PP. Sampling properties of the spectrum and coherency of sequences of action potentials. Neural Comput. 2001 Apr;13(4):717-49.
Tallon-Baudry C, Bertrand O, Delpuech C, Permier J. Oscillatory gamma-band (30-70 Hz) activity induced by a visual search task in humans. J Neurosci. 1997 Jan 15;17(2):722-34.
Knosche TR. Transformation of whole-head MEG recordings between different sensor positions. Biomed Tech (Berl). 2002 Mar;47(3):59-62.
TF Oostendorp, A van Oosterom. The surface Laplacian of the potential: theory and application. IEEE Trans Biomed Eng, 43(4): 394-405, 1996.
F. Perrin, J. Pernier, O. Bertrand, and J. F. Echallier. Spherical splines for scalp potential and curernt density mapping. Electroencephalogr Clin Neurophysiol, 72:184-187, 1989.
Maris E., Oostenveld R. Nonparametric statistical testing of EEG- and MEG-data. J Neurosci Methods. 2007 Apr 10; [Epub ahead of print] http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17517438
Maris E., Schoffelen J.M., Fries P. Nonparametric statistical testing of coherence differences. J Neurosci Methods. 2007 Jun 15;163(1):161-75. http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17395267
Van Gerven, M.A.J., Jensen, O. Attention Modulations of Posterior Alpha as a Control Signal for Two-Dimensional Brain-Computer Interfaces. J Neurosci Methods. 2009; 179:78-84. url
Van Gerven, M.A.J., Hesse, C., Jensen, O., Heskes, T. Interpreting Single Trial Data using Groupwise Regularisation. Neuroimage. 2009; accepted for publication.