Indexes enhance query performance, often dramatically. It’s important to think about the kinds of queries your application will need so that you can define relevant indexes. Once that’s done, actually creating the indexes in MongoDB is relatively easy.
Indexes in MongoDB are conceptually similar to those in RDBMSes like MySQL. You will want an index in MongoDB in the same sort of situations where you would have wanted an index in MySQL.
See more on http://www.mongodb.org/display/DOCS/Indexes