Controlling Lync 2013 Client Behavior Through GPO's

The Lync 2013 client doesn't have as many in-band GPO options as previous versions of communicator did (hopefully MS will change that), but there are a few reg settings that you can throw into a GPO to control it.
 
Add these settings into your GPO as a User Setting.
 
Minimize to the notification area instead of the task bar:
 
Navigate to:

HKCU\Software\Microsoft\Communicator\MinimizeWindowToNotificationArea

Set the value to 1 - Lync is minimized to the notification area when the Contact List is closed


Automatically start Lync at logon:

Navigate to:

HKCU\Software\Microsoft\Communicator\AutoRunWhenLogonToWindows

Set the value to 1 - Lync starts when you log on to Windows


Auto Open Main Window When Startup:

Navigate to:

HKCU\Software\Microsoft\Communicator\AutoOpenMainWindowWhenStartup

Set the value to 1 - Show Lync in foreground