Here's an abstract from a recent 10gen event presentation suggesting that mind maps are the most logical tool for the job. I expect more specialized tools to emerge, but in general, mind maps align well with non-relational schema design.
"Most of us are visual learners. Often, visual learners will find that information "clicks" when it is explained with the aid of a chart or picture. For MongoDB that picture is a leaf representing a natural approach to databases. In the RDBMS world a database schema is "visualized" through an Entity Relationship (ER) diagram. An ER diagram is the primary communication tool about an RDBMS data model. MongoDB provides a powerful dynamic database schema. However it is sometimes difficult to visualize. An accurate visualization of a MongoDB schema dramatically increases the ability to communicate the flexibility and power MongoDB between developers, architects, DBAs and end users. A mind map is a visual thinking tool that helps structure information, do better analysis, comprehend, synthesize and generate new ideas. Its power lies in its simplicity, much like MongoDB. Using a mind mapping open source tool, a clear and vibrant visualization of a dynamic MongoDB schema can be created that "clicks." Further, it works the other way around - mind maps can be used to create a dynamic schema in MongoDB. The mind mapping process allows non-technical business users to visually develop their requirements on the fly. During design process the mind map provides a flexible visual tool which changes in a fluid manner."