Build a test plan. Create a script that walks through your most common office tasks, both simple and more complex. Use it when you try out each solution, and you'll get a balanced comparison of how easy each package is to use.
Portability of data. If you leave, how easy is it to export your records to take them to new system? Remember that the patient data is yours, not the vendors: they need to be able to provide you with usable information if you decide to stop using their software.
Agree on your charts. Multiple physicians in the same practice often have different charting styles. Make sure you have a standard chart worked out before you start evaluating EMR software.
Go for the standards. Make sure any software you choose for your practice uses both SSL (for security) and HL7 (for seamless data exchange). These industry standards ensure that your system is dependable and built for the long haul.