What would you use for a brand new cross platform GUI app, CPython or IronPython ?
What about
 - license / freedom
 - development
    - - doc
    - - editors
    - - tools
 - libraries
 - performances
 - portability  
What can you do best with one or the other ?
 - networking
 - database
 - GUI
 - system
 - multi threading / processing
Use CPython, with IronPython you are bound to .Net platform which do not have much cross platform support, mono is there on linux but still for a cross platform app, I wouldn't recommend .Net.
So my suggestion is use CPython, for GUI use a framework like wxPython/PyQT and you would be happy.
CPython or IronPython?