Slashdot reported on D-Wave's recent demo of their 16-qubit quantum computing system. Video's of the demo can be watched on Google Video. The second video demonstrates the use of the machine in similarity searching:
Now, that screenshot does look like Jmol. The companies website does not give the answer, though Scott mentions C and Java front end software.
So, let's ask the source: Dear dr. Rose, is it Jmol what we see in that demo?