This is where I was talking about reality. Powerful commodity hardware killed Cray and SGI, not Linux. Pentium computers with workstation graphics cards costing only a few thousand dollars ended up being more powerful than ten thousand dollar MIPS machines with custom graphics. The Opteron caused Cray so much headache in HPC that they actually jumped on the Opteron bandwagon themselves.
Without Linux, those U.S. supercomputer companies don't go bankrupt. Foreign governments don't instantly have the ability to build their own supercomputers, either. These are two unfortunate results of the introduction of Linux, whether you continue to deny the obvious exact relationships or not.
Absolutely. The new Cray stuff is pretty cool, even though they are now using commodity CPUs. They have a lot of experience tying multiple processors together with wicked fast backplanes. I recall seeing some stuff about their design process and it's pretty cool. If Cray can benefit from the cost reductions and economies of scale that are facilitated by using OTS components, they should continue to do o.k. They probably won't regain their previous stature of being the best supercomputer on the planet, but if they can't keep up, then they don't deserve it anyway. I always wanted one of those Cray computers that look like a round couch. :-)