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I also thought that the highest level of scientific computing ... usually in huge superclusters - to do the heavy number crunching their disciplines required (think of where UNIX was first developed and evolved).
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I am a little late into this discussion.
I am one of those persons who carries the title of nuclear physicist. I have the piece of paper collecting dust somewhere.
I work with a few labs. Specifically, Notre Dame, Yale, Berkeley, and Argonne National labs. I will get to add Pacific Northwest National Labs to that list if my trip next week goes well.
All of these labs use mostly Linux. In particular Red Hat variants. Some use enterprise (Yale) others use Scientific or Fedora. There are still some machines that run some older version of Unix that are being phased out. Argonne was using Solaris, but now they are migrating to Red Hat Enterprise the last time I was up there.
Yes, all of our processor intensive applications are run on Linux clusters. We are fortunate to have one here. These are generally used for theory modeling calculations.
From what I have seen is the main reason we use Linux is cost, and the availability of developer tools. Most of our software is custom made. We are not a large enough market to justify forming a company to make it for us. Also most of it was originally written in Unix, and we want to continue to use it instead of investing the time to re-write the code. In addition to that we would be very hesitant to spend money on software versus a new piece of equipment. To complicate things even further we often have to modify our programs to analyze the data for different situations. Although that situation is improving (see Root, no not root user it is a software program). Another thing you may notice is they generally install a version of Linux and leave it. I am using Red Hat 5.1 (not sure about that version number it uses Nautilus 1.0.4) on one of my work machines.
I should also mention that the vast majority of people still use Windows. Most people have a laptop that runs Windows or dual boots with Linux. Then there is the Linux desktop used for analysis and work. Windows is mainly used for Power Point and the Adobe products for work items.
I should also mention due to the power and affordability of laptops more and more people are shifting all their work with the exception of intensive calculations to exclusive use on their laptops. That way you can carry your work with you.
The secretarial and support staff all run Windows. In the administrative area is Windows dominant. Those admin guys insist on sending me Microsoft Word documents and then get irritated when they don't print out like they should, even though all I have is a Linux machine with a very old version of Open Office.
The bottom line is that we have to get work done and publish results. We use whatever will help us achieve this the best. In general we don't care about the software or who makes it as long as we can afford it and it gets the job done. We want it to work as quickly as possible as cheaply as possible.