We currently have a large Cisco Enterprise cluster that we built a large Microsoft Lync cluster on top of. We use Lync now to deploy end users with phone capabilities and use cisco for all analog/routing.
Works pretty slick.
what phones are on the desktops and what do they register to?
We elected to go with Lync phones so users had a single experience. We use the VVX300/VVX400's and usually only reserve them for an absolute need case. (Speakerphone in office, Plant Director, etc) They are cheaper than Cisco phones even on the used market, but take a bit to get the provisioning set up correctly.
We try to do 90/10 % Headset users to hardphone users for cost savings.