The Matlab loaddap Tool provides a way to read any DAP-accessible data into Matlab. This is the second major update to the older 'Command Line Tool' and this version adds the ability to preserve structures in data sources by creating Matlab Structure variables where appropriate. This version should be used in place of the older 'Command Line Tool' where possible. We're maintaining the older version as resources permit. You can use the tool within scripts.
Also note that Matlab 2012a Includes Built-in Support for OPeNDAP! This capability takes advantage of new features in the netCDF C library developed by OPeNDAP and Unidata under support from NSF. The blog post includes a tutorial using same data from our test server.