This is one of the most innovative ideas I've ever seen on vBulletin.org. Along with Logician's dynamic templates this will be one of my most happiest installs. I can see a few potential flaws whilst looking at the code. Would be nice to do command permissions via usergroup or individual users. Also i'm sure there must be some better way of storing the commands in the database other than in the $DB_site->query() format. I can't think of the top of my head but it seems like an obvious security flaw. Perhaps hashing the query would a bit more secure.
Also how about a command creator. You enter your table/tables which you wish to perform commands for the particular command. Then for each table you select you have a dropdown for UPDATE,INSERT,DELETE FROM, and so on. Then you have a selection of where clauses where it detects the fields from the table and you have a dropdown for those.
Maybe i'm getting carried away but I just love the idea of this modification
All the best,
- Dean