Most Exchange Server 2000 installations run on Windows Server 2000. At some point, an administrator will want to upgrade to Exchange Server 2003 along with Windows Server 2003. To do this, however, the migration needs to be approached from the inside out: Exchange first, then Windows.
The first reason for this: Exchange Server 2000 does not run on Windows Server 2003. If you attempt to install Exchange Server 2000 in Windows Server 2003, the install process itself may fail. The same goes for attempting to upgrade a Windows 2000 installation with Exchange Server 2000 on it--if you attempt to do an in-place upgrade to Windows Server 2003, the upgrade will abort with a warning.
For those who want to perform an in-place upgrade to Exchange 2003 and Windows Server 2003, this will be a multi-stage process. First, back up all the relevant data on the server. Second, run the Exchange 2003 upgrade, which is essentially the same as installing Exchange 2003 on top of Exchange 2000. All mailboxes and other relevant data and settings should be preserved intact. Finally, upgrade the server itself to Windows 2003.
If another machine in the organization is the domain controller and you're planning to migrate that to Windows Server 2003 first, remember that the Exchange 2000 version of the Active Directory connector doesn't work with Windows Server 2003. It does work in a mixed-mode domain environment, however, but with some preparation. Microsoft Knowledge Base article 325379 contains extensive details on how to allow Exchange 2000 to seamlessly interoperate in a mixed domain that is being migrated to Windows Server 2003 (look under the header "Upgrading Windows 2000 Domain Controllers to Windows Server 2003").
The second reason: Some Exchange 2003 features will not work on Windows Server 2000. Some of these features are RPC over HTTP access from Outlook 2003, the SharePoint Portal Server, IPSec support for clustering, cross-forest Kerberos authentication, and the Volume Shadow Copy service. (You can see a complete list of the Exchange Server 2003 features supported by Windows 2000 Server at http://www.microsoft.com/exchange/evaluation/features/win_compare.asp).
If you are planning to implement any of these features -- especially Volume Shadow Copy, which is an integral reason to migrate to Windows Server 2003--you will need to wait until Windows Server 2003 is completely set up before attempting to implement any of these features.
Serdar Yegulalp is the editor of the Windows 2000 Power Users Newsletter.