Upgrade to 4.6.16+ caused site to fail with error
This is a JIRA ticket here which references a patch that others have said has fixed things. I just tried cherrypicking the changes over and then run drush cc but still seeing same errors. 

clearly relates in my case to a contact_sub_type that looks like it had its name changed (in contact_type I am seeing label = Funder. and name=Funder_ but in custom_group it is just referred to as Funder)

I did try changing the contact_type name from Funder_ to Funder but no joy

EDIT: actually i think renaming did succeed, as i then reversed the patch out, for the sake of something else to try, but same error on drush cc - and then on a whim visited civicrm/upgrade, and while that page told me "Your database has already been upgraded to CiviCRM 4.6.16.0" it did the job, and the resolved alerts flooded on to the phone etc.

Hope that gives you some clues.

Also, in case it has any relevance, the sub-type that caused the problem had "CiviEngage - Funder" in the description, so wondering if the misnamed type came as part of that? Maybe worth checking.