If you have some experience with Python (or even not), I would recommend using the Python scientific software that is available ([SciPy][1],[Pandas][2]),...) together with [Matplotlib][5]. Being a programming environment, you have full control over your data flows, data manipulations and plotting. You can also use the "full applications" [Mayavi2][3] or  [Veusz][4].


  [1]: http://www.scipy.org
  [2]: http://pandas.pydata.org/
  [3]: http://code.enthought.com/projects/mayavi/
  [4]: http://veusz.github.io/
  [5]: http://matplotlib.sourceforge.net/index.html