This latest version of the command line utilities adds the capability to generate Schema Diff and DGML database graph files.
The schema diff option allows you to compare a SQL Server Compact database file with another SQL Server Compact database file or even a SQL Server database, and creates a script with the required ALTER TABLE etc. statements to synchronize the 2 database schemas.
The DGML option allows you to create a graphical view of the database tables and fields, the resulting .dgml file requires Visual Studio 2010 Premium or higher to be viewed. I blogged about DGML files earlier:
The latest documentation for the command line utilities is available here.
And both these file types can of course be generated from your own application, using the scripting library. I have some code samples available here.