There are multiple ways to do this. Probably the simplest is to have three different folders, each containing their own CrmSvcUtil and their own config file. Then in your Post Build Command line (or if you want to run it manually create a batch file), enter the paths to your 3 different CrmSvcUtil's:
"$(TargetDir)\Project1\CrmSvcUtil.exe"
"$(TargetDir)\Project2\CrmSvcUtil.exe"
"$(TargetDir)\Project3\CrmSvcUtil.exe"
Each one will run by itself with it's own settings, and can output it's own context file.