From the top of my head Marnoch (church built in the circle), Kinellar (church wall built on top, you can still see the recumbent). Leochel-Cushnie Church is built beside one and on top of a another cairn!
Hi Drew
Dunno if you've seen this thread: http://www.themodernantiquarian.com/forum/?thread=23749
You should add yours to it! It's a fascinating subject, innit... There's a surprising amount of 'em when you start looking. :)
G x