I've been talking a lot about zero-downtime deployments with MySQL as your database backend (including schema changes/migrations!) recently.
I gave a 45 minute presentation called Zero Downtime Deployments with Database Migrations, from a DevOps conference that Vladimir Vuksan and I organized back in November 2012.
Feel free to drop me an email if you need help with implementing zero-downtime deployments or schema changes in your own applications.
Finally, here are a few more useful resources: