Conda (http://conda.pydata.org) is a more general packaging format than wheels and we use it to distribute the Scientific Python Stack (including complex C-dependencies) with ease. It is more general than wheels and solves this fundamental problem now with all the benefits without waiting for something in the future. See these blog-posts for more information: http://www.continuum.io/blog/conda_packaging and http://technicaldiscovery.blogpost.com

In particular look at the `conda package` command for an easy way to bundle up any non-conda packages across a homogeneous environment.