One of the great features released with the Microsoft Dynamics CRM Polaris update is the Skype Integration. Before Skype integration was available you were able to click on a phone number and dial out via Lync.
If you noticed that your default App is now Skype and would like to switch that back to Lync, follow these steps:
Within Microsoft Dynamics CRM, Navigate to Settings -> Administration -> System Settings.
Scroll down on the General tab and select 'Lync' under the "Set the Telephony Provider" section: