Ok so you narrowed it down to one site now. What plugins do you have that are active. Actually any deactivated plugins I would remove because even though you deactivate a plugin, if its a bust of a plugin, well it'll still keep up with its damage even after being deactivated.
There's a lot here that is running. However we sure know its MySQL being affected and something is eating your DB up.
I sear I had this same problem with a site I managed, it would work for couple hours and MySQL would crash, reload and its running for a few hours again. If I could just remember the fix ohhhh grrr. :)