If what you want to do is to compare the table structure,
SQL::Translator may work for you. Pretty impressive project. It has a sqlt-diff tool which can be used to create alter scripts between schemas.
I researched this the other day, looking for a tool to help upgrading schemas, and my impression is that the capabilities seems a bit spotty, and the database support is somewhat uneven. If you use MySQL it may work just fine, if you use Oracle (like I do in the current project) or some other database, it may depend on what features you use in the schema. For example, the Oracle diff seemed to lack support for sequences and partitions, just to name a few things.
(One other tool I looked at briefly is Embarcadero Change Manager, which looked very competent and feature-complete. It operates on db connections though, not SQL DDL statements which I would prefer.)
/J
