Hi! I finally figured out what was going on. Thanks for the people
who gave suggestions.
The query I thought was the problem really wasn't -- at some point
between 5.0.13 and 5.0.22 a change was introduced which affected
inner joins. I had a view which was aggresively created using inner
joins (in order to take an EAV-like table and view it as though it
were a regular table), and if I tried to do a three table inner join
with a view involved, it sat there and entered some kind of loop.
This either caused the tables to be locked, and later queries
involving these tables were waiting for a freed lock, or eventually
the number of open connections / threads climbed too high and all
later connections were waiting. I was able to (for now) solve the
problem by recreating the view as a realized table which gets rebuilt
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