GEDMatch is completely free (although donations are much needed and appreciated) and independent of the testing companies.
If Ancestry gives us our raw data in a downloadable format, then we'll be able to use it several places for free. (I don't know what tweaks might be necessary from the third party tools to make that happen smoothly, if tweaks are needed at all.)
Here is a list of third-party tools from the ISOGG site: http://www.isogg.org/wiki/Autosomal_DNA_tools
Maybe Ancestry will implement some of these features into their own interface - I like seeing all of these companies stay competitive! :)