Our Windows NT 4.0 domain structure includes separate domains for our Exchange servers. Should we carry that design forward when we migrate to Exchange Server 2003?

You shouldn't carry forward any NT 4.0 domain design if you can avoid doing so. The use of resource domains that contained only resources such as Exchange or Microsoft SQL Server servers and not user accounts was common with NT 4.0; however, implementing these types of domains is no longer considered to be a best practice. When you use Active Directory (AD), you can place your Exchange servers in organizational units (OUs). This configuration avoids the need to create separate domains, which in turn restricts the number of people who must be given Domain Admins permissions. By putting your Exchange servers in their own OUs, you can still delegate control over the servers to the Exchange administrators while retaining domainwide control. You can also use Group Policy Objects (GPOs) to apply Exchange-specific policies to the Exchange OUs.