The MySQL slow query log could be of use. Of course you don't get a stack trace this way but it's essentially free (as in built already and not a huge performance hit).
Problem I have with this log is that legitimately slow queries, in my case usually those where I have concatenated 100's or 1000's or inserts into one query, make it hard to use in a meaningful way.
It's possible I'm using it wrong, did get much past trying it out. Fairly easy to roll my own rough timer in a DB wrapper, haven't got around to finishing this yet though.
