Rob adding text on 2/10/2017:
nuget.exe | dotnet.exe can now use encrypted passwords in nuget.config files -- when running on windows ONLY.
Ideally, we'd support dotnet.exe on other platforms too, so they don't need to store passwords via cleartext.

This would need APIs from .NET Core. See the related https://github.com/dotnet/corefx/issues/6746