Use a database specific function in dbtng (e.g. uuid in db_insert)
Here's what I ultimately did:

db_query("INSERT INTO {mytable} (uid, event_guid) VALUES (:uid, uuid())",
array(':uid' =&gt; $uid));


And that works to use the mysql uuid() function in an insert.

I've created an issue to add this to Drupal 8 http://drupal.org/node/1858188