I have a mongodb replica set with a lot of databases, collections & indexes.
We did a lot of refactor and optimization and, of course, I have a lot of \"creative
There is a pretty cool script out on Github that you should look at:
https://github.com/wfreeman/indexalizer
Basically it involves turning on profiling for your database and then it will use the data collected by the profiler to drive explain() calls. It then tells you both which indexes are not being used and which queries are not using indexes. Pretty slick.
More about mongoDB database profiling:
http://docs.mongodb.org/manual/reference/database-profiler/