At work, we use a modified version of DBIx::Migration (it has some limitations, such as no more than 10 migrations). Then, you have a core schema that you've dumped from your database and when the version number is too low, you upgrade your database using the migrations from the migration schema directory.
I also highly recommend the Database Refactoring book. Amongst other things, it will give you excellent techniques for managing migrations safely in such a way that if you need to roll back, you don't lose data (such as when you drop a column you think you don't need).
To help with the automatic deprecation schedules it suggests, I've written Devel::Deprecate so that you don't need to remember when to do the deprecations. Your code will complain loudly for you (and only in testing, not in production).
Important: You'll periodically find that you're applying so many database migration levels with this technique that you'll sometimes need to "bump up" your minimum base migration because it takes too long to rebuild the database. Just take a new dump of the database at the desired migration level and remove all migrations less than or equal to that level.