I've never heard of Cray using 68040's, they'd be far too slow. NCR did some unix boxes with them, but they were outclassed by intel pretty quickly.
I saw one on a documentary. It had a sign on it, "Cray supercomputer." Next line said, "68040"
Also I heard of a supercomputer - not sure which one using about 8 or 12 68040s, when the 68040 was brand new.