Flip3D isn't using WPF, but the Desktop Window Manager (the 3D desktop composition engine that makes Flip3D possible) is built on milcore, the unmanaged low-level engine that underlies WPF.
And yes, you can access and use the application thumbnails for your own purposes. You probably can't do this directly from a .Net application, but some PInvoking will get the job done.
The important functions to look at are
DwmRegisterThumbnail and
DwmUpdateThumbnailProperties. The first will tell the DWM "I want to show the thumbnail for window X on window Y" and the second will cause it to be drawn with the specified properties. Note that the documentation for both these functions (and the rest of the DWM) is still far from complete.