I have run the report testing for violated foreign key constraints on all our 730+ production moodles.
I've collated all the violated constrains using (http://cvs.moodle.org/contrib/tools/devtools/xmldb_refintegreport.php) and then aggregated all the data from all the moodles and produced a summary report which is attached.
As you can see the grade-book is the major offender here.
This data is from quite a wide cross section of sites, from heavy users upgraded from external hosts on < Moodle 1.4, to brand new installs on 1.9.3. (All are now on 1.9.3).
230ish didn't have any violated constraints at all