This is not a comprehensive list of available and evolving standards, please feel free to add more pointers.

HITSP (Health Interchange Technology Standards Panel). Free specification. I heard about this during a really interesting talk on the unintended consequences of healthcare IT. It's worth listening to.

Also, SmartHealth and Indivo.

http://www.mobih.org/

http://indivohealth.org/research - They have RDF/python implementations for a full stack, although PHR codings are proprietary.

It'd be great to have compatible codes that were "open."