Our win32 application assembles objects from the data in a number of tables in a MySQL relational database. Of such an object, multiple revisions are stored in the database.
I've looked into MysQL Diffing a number of times. Unfortunately, there aren't any really good solutions available.
One tool I've tried was mysqldiff (www.mysqldiff.org). mysqldiff is a tool written in PHP which is capable of diffing mysql schemas. Unfortunately, it doesn't do a great job a lot of the time.
MySQL Workbench, MySQLs own SQL IDE provides the option to generate an alter script and I would imagine it does this by performing some kind of diff operation internally.
Aqua Data Studio is another tool that is capable of comparing schemas and outputing a diff of the two. While the ADS diff is quite nice, it does not provide a tool to create an alter script.
If I were writing my own I guess I would write code capable of comparing structure of two tables. Such code could be tuned to be highly sensitive (Ig if column order differs from from version to the next, it's a difference) or more moderately sensitive (Eg Column order is not a major issue, datatypes and lengths are important, as are indices and constraints).
Storage, I'm not to sure. I would look into how a version control system such as Mercurial stores its diff information for revisions and use that to elaborate a method appropriate for the DB.
Finally, for visual output I recommend you take a look at the Aqua Data Stduio compare feature (You can use the Trial version to test this...). Its diff output is pretty good.