Where I'm coming from: I'm a satellite physicist working as a contractor for the USGS on the Landsat program. I work very closely with NASA.
Almost all the scientific programming we do -- and by 'we' I mean USGS and NASA -- is either in IDL/ENVI or Matlab. They're the defacto standards for scientific processing. We do need to know SQLPlus to get our data out of the databases, and we need rudimentary C++ skills in order to make prototype code for the IT coders to turn into an operational release. Sometimes it's easier to code something in C++ then IDL or Matlab, so it's nice to be able to jump straight to that when warranted. Add Perl for text manipulation (which always turns out to be useful in some way) and that's all the programming I've done for the past ten years. Many scientists in the building swap out ARCGIS or ERDAS for IDL/ENVI. (Matlab doesn't seem to be swappable; you either need to use it or you never touch the stuff.)
I've dabbled in Php when they asked me to prototype a web site but that never went far. I've done a little Flash programming that they eventually decided to hire out for. (I did a fine job, but they wanted the application to go bigger.) In the early days of my career FORTRAN was everywhere, you couldn't get away from it. There are still some FORTRAN programs in-house that I could fiddle with if they asked me to, although I'd blanch at the prospect.
All that said, what you need depends on what your role is. If you're a scientist like me then these self-taught languages might be enough. If you're a science-oriented IT person, you'll need more -- most importantly strong C++ skills, at least around here. And different disciplines will have different needs; I worked briefly for NIH (National Institutes of Health) and they still had COBOL programs.
I know of one person in two organizations (USGS and NASA) who knows Python, and he's an IT guy not a scientist. He's also the only person I know who has ever used Hadoop. I have never met anyone who knew R. Visual Basic is used occasionally here and there for prototyping, and almost immediately switched out with C++ as soon as management decides to support the project.