We got some of the first ones at the Naval Research Laboratory in Washington, DC, and I used them to perform (unclassified) molecular dynamics simulations. People used them to scale up all kinds of simulations. The language was a special dialect of C called C*, which was essentially C with array extensions that made doing arithmetic on the CM (which, as other commenters point out, was really just a big array processor) relatively easy to program. It was a single-instruction-multiple-data model, where each little processor got its own piece of the array. Then as now, the way to get speed was to minimize communication among processors.
Whatever your feelings about the NSA, it's an extremely cool museum, and free admission (at least when I went). The staff are incredibly knowledgeable, while obviously they can't discuss classified material, you're bound to get some great unpublished tidbits from them.
They were instrumental in a certain theme park, but the lead programmer suffered an unfortunate… workplace incident as he was attempting to commit industrial espionage. The Costa Rican government has kept this quiet since the 90s…
