A general question, without a specific case in mind - is it usually preferred to use MySQL stored procedures over writing a PHP script that performs the same calculations an
I think Jeff Atwood hit the nail on the head in 2004 regarding stored procs:
Who Needs Stored Procedures, Anyways?
Having used both stored procedures and dynamic SQL extensively I definitely prefer the latter: easier to manage, better encapsulation, no BL in the data access layer, greater flexibility and much more. Virtually every major open-source PHP project uses dynamic SQL over stored procs (see: Drupal, Wordpress, Magento and many more).
This conversation almost seems archaic: get yourself a good ORM, stop fretting over your data access and start building awesome applications.