Start with data standards, and build them transparently. Many state and federal agencies are making calls for adoption of standards in data publication, to save time designing and implementing interoperability, or simply compiling data from different jurisdictions for federal reporting.

See the recent call by the US DOT for agencies to adopt and publish transit data using the GTFS data standards (originally developed by Google for streamlining consumption of transit data )from different agencies. http://gis.rita.dot.gov/Transit/downloads/DearColleague.pdf

BLDS Specification originally developed by Accela for building permits. Now many competitors are signing on and adopting the standard. http://permitdata.org/