just to answer questions... we tend not to use transactions, stored proceedures, foreign keys, constraints and cascading deletes because honestly... mysql sucks at being a "grown up" database... plus most of them are rather new features anyhow.. if we desired a strong DB, we would use postgres.
mysql is fast, and what makes it fast is that it dosent support (or at least didnt used to) all of the features listed above. I do agree that external utilties is the safest way to "clean" the DB of crap which might build up over time. That said, nobody is running a server (and likely ever will) on a large enough scale to make cleaning the DB really matter.
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