Posted this on the wrong thread (extensions), posting here and deleting there... I'm not sure if anyone has done anything similar, so I went ahead and did it myself - created VQMOD that logs the execution times of each query that runs ($this->db->query).
I found it extremely helpful for optimizing my DB, creating new indexes that aren't present in the base install, along with several modules which had great functionality but not so great database access.
If anyone is interested - I posted it to GitHub - figured not to put it on the OC Marketplace, because out of fear that regular users might try to use it (it definitely has a impact on system performance).
Would love feedback.
(will be posting a few more things that that GitHub account in the next few days as well)