If you use the method LORETA (any implementation, any other software package), then it would be appropriate that you quote:
1. Pascual-Marqui RD, Michel CM, Lehmann D. Low resolution electromagnetic tomography: a new method for localizing electrical activity in the brain. International Journal of Psychophysiology 1994, 18:49-65.

If you use the LORETA-KEY software package, then it would be appropriate that you quote at least:
1. Pascual-Marqui RD, Michel CM, Lehmann D. Low resolution electromagnetic tomography: a new method for localizing electrical activity in the brain. International Journal of Psychophysiology 1994, 18:49-65.
2. Pascual-Marqui RD. Review of Methods for Solving the EEG Inverse Problem. International Journal of Bioelectromagnetism 1999, 1:75-86.
The first paper refers to the method, the second to its implementation in the digitized Talairach atlas that is used in the LORETA-KEY software.

If you use TANOVA (topographic analysis of variance), then it would be appropriate that you quote:
1. Strik WK, Fallgatter AJ, Brandeis D, Pascual-Marqui RD. Three-dimensional tomography of event-related potentials during response inhibition: evidence for phasic frontal lobe activation. Evoked Potentials-Electroencephalography and Clinical Neurophysiology 1998, 108:406-413.

If you use frequency domain analyses, then it would be appropriate that you quote at least:
1. Pascual-Marqui RD, Michel CM, Lehmann D. Low resolution electromagnetic tomography: a new method for localizing electrical activity in the brain. International Journal of Psychophysiology 1994, 18:49-65.
2. Pascual-Marqui RD. Review of Methods for Solving the EEG Inverse Problem. International Journal of Bioelectromagnetism 1999, 1:75-86.
3. Pascual-Marqui RD, Lehmann D, Koenig T, Kochi K, Merlo MCG, Hell D, Koukkou M. Low resolution brain electromagnetic tomography (LORETA) functional imaging in acute, neuroleptic-naive, first-episode, productive schizophrenia. Psychiatry Research-Neuroimaging 1999, 90:169-179.
4. Frei E, Gamma A, Pascual-Marqui R, Lehmann D, Hell D, Vollenweider FX. Localization of MDMA-induced brain activity in healthy volunteers using low resolution brain electromagnetic tomography (LORETA). Human Brain Mapping 2001, 14: 152-165.
The first paper refers to the method; the second to its implementation in the digitized Talairach atlas that is used in the LORETA-KEY software; the third to the first publication with frequency domain LORETA; and the fourth to the detailed computations of frequency domain electric neuronal generators.

IN ADDITION to the previous references, if you use any of the statistical analysis tools, then it would be appropriate that you quote at least:
1. Nichols TE, Holmes AP. Nonparametric permutation tests for functional neuroimaging: a primer with examples. Human Brain Mapping 2002, 15:1–25.

If I were asked by a reviewer why I used LORETA instead of other methods, I would reply (approximately):
If brain activity is spatially distributed and not confined to single point sources, then a distributed EEG/MEG tomography is more appropriate than dipole fitting. Of all published 3D, discrete, distributed, linear EEG/MEG tomographies, LORETA has the lowest localization error [1,2], except for sLORETA [3].
1. Pascual-Marqui RD. Review of Methods for Solving the EEG Inverse Problem. International Journal of Bioelectromagnetism 1999, 1:75-86.
2. Pascual-Marqui RD, Esslen M, Kochi K, Lehmann D. Functional imaging with low resolution brain electromagnetic tomography (LORETA): review, new comparisons, and new validation. Japanese Journal of Clinical Neurophysiology 2002, 30:81-94.
3. Pascual-Marqui RD. Standardized low resolution brain electromagnetic tomography (sLORETA): technical details. Methods & Findings in Experimental & Clinical Pharmacology 2002, 24D:5-12.
The first paper compares LORETA with all published inverse solutions up 10 1999. The second paper compares LORETA with the method of:
Dale AM, Liu AK, Fischl BR, Buckner RL, Belliveau JW, Lewine JD, Halgren E: Dynamic statistical parametric mapping: combining fMRI and MEG for high-resolution imaging of cortical activity. Neuron 26: 55-67, 2000.