Kurt,
Are you in Crisis mode or is this a situation where you're trying to create
a cogent backout plan in case things don't go well.
Generally, I would suggest making sure that you have verifiable backups.
From there, I would take a BDC off-line and add a W2K/W2K3 server to the
domain as a member server and promote from there.
If you have segregated user and resource domains, I would do the Users
first, then work with the resource domains. This would give you the
immediate benefits to your user and workstation management and buy you some
time on testing and implementation of your apps in the AD environment.
Generally, though, applications don't have a problem with this unless they
are accessing the SAM database in NT or rely specifically on the NT os for
client server components.