I administer an inherited Exchange Server environment. The previous administrator created a Recipient container for every department instead of using Address Book Views. Can I merge all the mailboxes back into one container during the migration from Exchange Server 5.5 to Exchange 2000 Server?

Fortunately, yes. Assuming that you're going to use the Active Directory Connector (ADC) during your migration, all you need to do is create a connection agreement (CA) that specifies multiple source containers on the From Exchange tab, then points to a single OU as the destination. If you want finer-grained control, you can always create separate CAs that point from the various recipient containers to the Users container in Active Directory (AD).