I think you should look at http://sqlfairy.sourceforge.net. It knows how to parse SQL into a data structure which should be fairly easy to compare, and can generate SQL from a data structure you build.
Comment on Re: Automatically altering tables from different schema's
I think I will need me to get SQL::Translator and start providing some patches ;-). Thanks for the tip, that was the module that I missed when doing my research into this area.