Microsoft has a utility for Exchange 5.5 called MoveServer. It is a very big job and you had better have a good backup, but I have used it successfully. I would not want to leave my users on that server and would decommission it after moving them across to another server. And per my assumption above, you would soon be moving them anyway to new Exchange 2003 servers.
Exchange 2003 Service Pack 1 brings along some new options. Once you have installed your first Exchange 2003 server in the Same Organization (as your Exchange 5.5 Organization), you can use the new Site Consolidation Tools in SP1 to MoveMailbox between Sites and Routing Groups. So if your goal of consolidating is to simplify your Exchange 2003 world, you could do it as part of your overall migration.
If the goal is to consolidate on Exchange 5.5 and wait a while (I am sure you know by now that support including security patches for Exchange 5.5 disappears at the end of 2004 for all but a few customers who can afford a final year), then you might try what I am about to suggest--but please note that this needs to be tested. Once you have installed that first Exchange 2003 server, you can use MailMailbox in Service Pack 1 to move across sites as described above. From the looks of the UI, you might be able to move from one Exchange 5.5 server to another Exchange 5.5 server. Again, you would have to test this.
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