Unused indexes are dead weight. How much it hurts it is application dependent but if you do not have a discipline dealing with it over years you may get too much of it.

Unused indexes slow down inserts but they also hurt selects because they waste time in caches. They also make MySQL optimizer to consider more choices than it needs to.

Finally disk space also means less hardware requirements and faster backups and other operations (such as cloning the slave)

Of course your millage may vary.

This works for both MyISAM and Innodb tables. As I mentioned this requires Percona Extensions to work. See the link in the bottom of the page.

I remain skeptical of the utility of dropping unused (or rarely used) indexes.

The load on most web applications is heavily weighted towards SELECT operations and there’s little downside to having “too many” indexes in that case. Only thing its really going to cost you is insert/update/delete time and some disk space.

To be sure, there will be cases where you’ve got an update bound workload and removing useless indexes is the solution, but, at least for the kind of applications I work with, that’s very much the edge case.