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 every hour.

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