That's a great question. I think any advanced space-faring civilization would have no further use of programming languages as we know them, as any ship or computer system would be sentient or even sapient by their builder civilization's standards. Communicating with these artificial minds would be as difficult as communicating with the aliens themselves.

We would have to overcome whatever language barriers we find before being able to do the equivalent of "programming" - I don't think there would be any language below whatever their equivalent of microcode though, nor do I think any language could express everything necessary.

Well, maybe Lisp ;-)