If you use m4s2 please cite:
T. Antao, A. Beja-Pereira, and G. Luikart (2007). MODELER4SIMCOAL2: A user-friendly, extensible modeler of demography and linked loci for coalescent simulations. Bioinformatics, advance access, doi:10.1093/bioinformatics/btm243 .

Most probably you will also want to cite SIMCOAL2:
Laval, G. and Excoffier, L. (2004). SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics, 20(15), 2485-2487.

Probably you will also want to site ARLEQUIN3:
Excoffier, L., Laval, G., and Schneider, S. (2005). Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50.