Like most Microsoft applications, Lync Server 2010 depends heavily on Active Directory to authenticate users, find server pools, and generally keep data flowing. As such, it is critical to account for this when planning a Lync Server 2010 deployment of any kind. Plan to upgrade legacy domain controllers and be aware that Windows Server 2003 mixed mode is not supported by Lync Server 2010.
One of the best things you can do prior to a large deployment into Active Directory is to perform an Active Directory health check. This involves reviewing event logs, running tools such as DCDiag and NetDiag, and checking replication health to ensure that the directory itself is healthy and operating correctly.