I can list three ways to interact with active plots:
1-) Using keyboard shortcuts: Changing scaling using "k" and "l" keys are my favorite. See more at http://matplotlib.sourceforge.net/users/navigation_toolbar.html
2-) Using the interactive navigation toolbar and with a small extension written by Pierre Raybaut (on Qt4Agg backend) For a screenshot see http://img156.imageshack.us/img156/9210/mplqtextra.png
This is open to development. Actually many of the command line mpl interface could be integrated into that window.
3-) Directly from within IPython shell. That's another useful way of updating figure properties (e.g. adding labels, changing font) IPython and matplotlib are very well integrated in that manner. Similarly, Mayavi does a great job of integrating shell and UI.