For a while now, I've really been digging what Liquidware is doing with ProfileUnity and Stratusphere.  But have you checked out FlexApp? 

App Layering is a hot topic these days.  And FlexApp from Liquidware is right up there.  This is a great way to have App Layering work with published apps out of the box. 

Want to know more?  Watch this video which goes into more detail about some of the new features such as "On-Demand Click-to-Layer" options and "Per User Session Isolation for Citrix XenApp and Microsoft RDSH."  And after the detailed explanation, keep watching the video for a really great demo from Jason Mattox.