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I have used both. I implemented a prototype back-end in CouchDB, and it worked well for this purpose, allowing me to get up and running quickly. But I found that I needed a couple of things that they didn't support - for example, I wanted to integrate with an existing authentication system rather than use the built-in CouchDB one. It became clear that I would have to write my own middleware layer in Python or similar. Once I had made that decision, I had lost the simplicity that is CouchDB's most compelling feature and I felt I was missing out in other ways - CouchDB's REST API is less flexible than MongoDB's programmatic API for example. So I switched to MongoDB.

I'd say both gave me exactly what I needed at different times, and so I recommend both projects highly, depending on what you need. CouchDB is an excellent tool to quickly "mock up" a live back end, and a great way to learn hands on with document stores with very little upfront effort required. MongoDB seems to integrate better as part of a larger system, and provides more flexibility.

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