Thanks davidj... I do understand the use of the explain syntax; I was thinking more along the lines of a switch or something that you turn on on the mysql server which would log which indexes are used... I envisioned running with this switch on for some period of time (say a week or two) and then examining the logs to see which indexes are always used, so I can know which aren't.

Most of the queries that are run against the server are dynamically generated, so it becomes difficult to pull them and do an explain on each... Especially since there are probably 50+ programs that access the database, each with 30 -50 different queries being run...