It needs top be able to export in multiple electronic formats, including x12, ansi, and all the others I am not thinking of right now.
It would be nice if it dovetailed into office ally since they have a no fee structure, but it should be compatable with most if not all clearinghouses.
It would be wonderful if it could bill based on the reimbursement, as Leslie stated, thus with multiple fee schedueles, you would have little to adjust as the fee matched the payment. I have not seen this in many programs.