Evaluating document-oriented storage, what are the pros and cons of CouchDB vs MongoDB?
There are a lot of differences between the two of them. MongoDB is more like a traditional RDBMS (nobody shoot). CouchDB performs master-master replication. It's pretty well documented in this much ballyhooed blog post.
Both are currently evolving, so if you chose one today, you may find that you need to switch later.
I know of a company that did a thorough review of both, with prototype apps implemented in both, and they made a well-informed choice based on the project requirements. Initially, they had success with their choice, but after about 6 months, some of the requirements were more fully understood, and they ran into a problem. Now, they are migrating to other db. During those 6 months, the other db added some features that allowed the company to overcome its problem, but the chosen db maintainers had worked on different problems and feature sets.
In short, it seems to me that you need to dig in and see what works good enough for your project. Keep tabs on the other choices, so that if you encounter an impossible problem, you can decide if switching makes sense.