What a minute… I looked at your own link and found that the source code is available:
http://www.research.rutgers.edu/~ionescu/iperf-wince/iperf-windowsce.zip[
^].
And if this is the UI, and you need just the "command line application" (there is no such thing, for your information; absolutely any application can use command line) as in Linux, so, I can guess that in fact you need the application without any UI except console. How come it could be a problem for a software developer? In this case, you don't need any new knowledge, you only need to simplify existing code.
If you face some particular problem, please ask a particular question; we would gladly help you.
—SA