GenStat citation
If you are using the menus, the best reference for GenStat is probably the introduction to GenStat for Windows:
Payne, R.W., Murray, D.A., Harding, S.A., Baird, D.B. & Soutar, D.M. (2006). GenStat for Windows (9th Edition) Introduction. VSN International, Hemel Hempstead.
If you are using the commands, you could cite the reference manual. In particular, if you are using a procedure, you should be able to find that (and refer to it) in Part 3.
Payne, R.W., Harding, S.A., Murray, D.A., Soutar, D.M., Baird, D.B., Welham, S.J., Kane, A.F., Gilmour, A.R., Thompson, R., Webster, R., & Tunnicliffe Wilson, G. (2006). GenStat Release 9 Reference Manual, Part 1 Summary. VSN International, Hemel Hempstead.
Payne, R.W., Harding, S.A., Murray, D.A., Soutar, D.M., Baird, D.B., Welham, S.J., Kane, A.F., Gilmour, A.R., Thompson, R., Webster, R., & Tunnicliffe Wilson, G. (2006). GenStat Release 9 Reference Manual, Part 2 Directives. VSN International, Hemel Hempstead.
(ed.) R.W. Payne & P.W. Lane (2006). GenStat Release 9 Reference Manual, Part 3 Procedure Library PL17. VSN International, Hemel Hempstead.
An alternative, for the commands and the underlying methodology, would be to refer to the Guide, e.g. you could cite the relevant chapter in Part 2 if you wanted to refer to a specific statistical area.
Payne, R.W., Harding, S.A., Murray, D.A., Soutar, D.M., Baird, D.B., Welham, S.J., Kane, A.F., Gilmour, A.R., Thompson, R., Webster, R., & Tunnicliffe Wilson, G. (2006). The Guide to GenStat Release 9, Part 1: Syntax and Data Management. VSN International, Hemel Hempstead.
Payne, R.W., Harding, S.A., Murray, D.A., Soutar, D.M., Baird, D.B., Welham, S.J., Kane, A.F., Gilmour, A.R., Thompson, R., Webster, R., & Tunnicliffe Wilson, G. (2006). The Guide to GenStat Release 9, Part 2: Statistics. VSN International, Hemel Hempstead.