phpBB 3.1 should include an easy way to migrate the database from one state to another. For phpBB 3.0 there is UMIL which takes care of this and can be used by MOD authors. It would be better to have this functionality in the core though, to ease distribution and to allow phpBB itself to take advantage of it.
UMIL handles both initial installation as well as updates to the database. Code and concepts can be borrowed from it.
Discussion of this ticket takes place in the RFC topic