In general, I very much dislike stored procedures because:
- It's too easy to slip in business logic that shouldn't be there.
- Updates to the application that require updates to your stored procedures is a pain to synchronize, especially if you have to revert to a previous build.
For any database manipulation, I recommend going with a PHP ORM framework like http://www.doctrine-project.org or a framework that includes ORM like CakePHP. You'll have an added bonus of being able to more easily switch between SQL Server and MySQL.