You should look at total storage size and total index size and make sure that they're not getting unreasonable for the amount of RAM you have.
It's not so much number of document as amount of data. You can run db.stats() to have a look. If writes are taking longer as you add data, it's probably because less data is fitting in RAM and more is having to be paged from disk. Are you doing a lot of updates or just inserts? Make sure that the query portion of the update is always using an index.
If you can provide db.stats() and db.collection.stats() along with info about your system, we can help more.