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-=HOAX=-,
MySQL is a very fast database. Sounds like one of two things is happening. Either your tables are not indexed properly for the queries you are running on them, or your system is running low on free memory causing MySQL to start swapping to disk which will *greatly* slow it down and cause a sort of thrashing symptom.
If you'd like, I can take a look at your system for you if you want to get in touch with me and give me a (non-root) login. My day job is a supercomputer sysadmin, so stuff like this is usually a piece of cake!
-skazzel
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