...and I would be remiss to fail to note that SAS PROC GENMOD rates highly in Horton,N.J. & Lipsitz, S.R. (1999) Review of Software to Fit Generalized Estimating Equation Regression Models, The American Statistician, 53:2, 160-169.
Of course, SAS also integrates spectacularly with JMP. There are a number of examples of SAS:JMP Integration starting on my page 590 in the Scripting Guide.
Good luck!