Cray is definitely using water cooling. I have a pic on my iPhone sent to me two weeks ago from a good friend who was a founding member of the Green Grid. Shows  their equipment with liquid cooling. his profession is data center cooling/power use and was in San Jose consulting on it.
useing Asetek liquid coolers. posting from an iPhone. may be I'll get around to posting it later.

http://www.asetek.com/#&panel1-3

 debateing an upgrade tonight or holding out for cointerra.