In my experience, using CouchDB for prototyping is not fun. With SQL and (from what I gather) MongoDB, you can create ad-hoc queries as you go. Creating views in CouchDB requires thought and time -- usually lots of time -- to generate the views, unless you're working with a very small amount of data. Changing your mind is painful. You end up using weird hacks to get around rebuilding your views all the time.
Maybe I was doing it wrong, but it seems like if your app has more than a little data and you plan on changing your mind about how best to present it, you will experience discomfort.
I don't have any experience with MongoDB, but I am building an application right now using CouchDB and I've found it to be pretty easy to use -- definitely easier to prototype with vs a relational database + ORM framework.
CouchDB supports ad-hoc queries in the form of 'temporary views'. The downside (and I think a difference compared with MongoDB) is that temporary views can't be used in production since they are not indexed and thus are much slower than permanent views.
I'm developing my application in Python, which has great support for CouchDB in the form of CouchDB-Python (http://packages.python.org/CouchDB/) and CouchDBKit (http://couchdbkit.org/). Using CouchDBKit, it was pretty easy to set up CouchDB artifacts (map functions, reduce functions, design documents) into a nice file/folder hierarchy and write the simple Python glue code to deploy updates to CouchDB via a single shell command.
so far we're going with couch and haven't experienced this. the best part of course is that we can add items to documents on the fly whilst keeping the existing test data! this is major for us. we can go back to testing right away. with MySQL the changes were so major that it was better just dumping and recreating from scratch (we are using django) and this wasn't exactly fast. django has a project "south" that would help with this, but we're eventually deploying to oracle and cannot rely on it or have the time to extend it to properly work with oracle.
Maybe I was doing it wrong, but it seems like if your app has more than a little data and you plan on changing your mind about how best to present it, you will experience discomfort.