We upgraded all our Microsoft Exchange Server 5.5 systems to run on Windows 2000. Now, we're getting ready to migrate to Windows Server 2003 and Exchange Server 2003. At what point during the migration should I apply the Exchange schema upgrades?

In general, the earlier in the migration you make the schema changes, the better. I suggest that you apply the schema updates to the first domain controller (DC) in your new forest because then each subsequent DC you add will receive the changes as part of its initial replication. If you wait until your DCs are in place before you apply the schema changes, you'll need to rereplicate every object on every Global Catalog (GC) server, which can be a burden to your network. The difference between these two approaches isn't in the amount of replication traffic, but rather the timing of the replication traffic: Upgrading the initial DC first spreads out the load.