For one, the creation of a single standard document for representing a medical history would go a long way towards enabling applications across the medical spectrum to coexist.
This document type does exist. Please review the emerging HL7 v3 documentation. Pay particular attention to CDA/CCD.
The bottom line is that once there is convergence around interoperability, which proprietary EMR solution a Healthcare Organization utilizes matter much less less. Prior to CCHIT and changes in STARK, vendors had little incentive to develop interoperable solutions - vendor lock-in is part of the HIT business model.
For once, the government is actually driving positive change into an industry. Through provider-based incentives (carrot vs. the stick), HCOs (Healthcare Organizations) will have positive incentive to implement interoperable solutions.
It's a facinating time in HIT, and I'm frankly enjoying being on the vendor side of right. I expect fundamental change over the next 5-7 years in HIT, unlike anything we've seen in the last 15. Great stuff, really.