Mirth is basically the default interoperability engine. Just as Apache is the default web-server.
ClearHealth, and OpenMRS are making improvements at a furious rate, and they are not the only good projects in the space.
We are getting closer and closer to having FOSS as first choice, and proprietary as second option.
(added 5-23-08) Thanks to Dr. Steve Watson who helped me with glaring grammar errors.