A bunch of enterprise services are Windows only. Also Active Directory is by far the best and easiest way to manage users and computers in an org filled with a bunch of end users on Windows desktops. Not to mention the metric shitload of legacy internal asp applications...
No not really. It does the various services for the most part, but Active Directory is exclusively a Microsoft product. Group Policy in particular also does not have a drop in replacement that's any sort of sane.
We run a lot of Windows servers for specialized applications that don't really have viable alternatives. It sucks, but it's the same reason we use Windows clients.
Basically AD and the workstation management that uses it. Could all be run on a VM and snapshotted because you know it's going to fuck up an update eventually. Perhaps SQL Server but that's getting harder to justify the expense of anymore.