System Center is the Microsoft umbrella brand for its management products. The tools behind Windows Intune are from System Center, so there is definitely an overlap. Windows Intune is a small subset of the functionality provided by System Center. System Center has not just the capability to manage and secure the desktop, but also back it up, deploy applications, and much more. System Center also manages all other Microsoft products, so it really does cover a much bigger target area than just the desktop.
The only time when Windows Intune and System Center being mixed together makes sense is when we are managing desktops that are not connected to the corporate domain or do not have access the corporate network. If this is not the case, it is unlikely we will mix these products on the same computer.
More information on System Center can be found at http://davidoverton.com/r.ashx?2K.
While Windows Intune is strictly aimed at policy and update management of Windows desktop computers...