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MongoDB has a reputation for being faster, while CouchDB has a good reputation for reliability, although older versions could be resource intensive. I think CouchDB is the only choice if you want offline replication. I think MongoDB is more like SQL (which is kind of funny since it is NonSQL). Keep in mind that neither are really suitable for financial transactions, if that is your concern you should probably stick with SQL.
A guy named Scott Motte did a comparison of MongoDB and CouchDB a while back. He is more knowledgeable than I am, and he put together a nice slideshow presentation. http://spitfiresky.com/blog/recap-of-my-sdruby-presentation-on-mongodb.html