It would seem to me that such a question is not explicitly prohibited by the FAQ, the first two "don't ask" examples would be the most relevant to consider:
- "What's your favourite ...?" might apply; though you're not strictly asking that, just for pointers to what's available it seems that "what do you use" is very close to "what's your favourite".
- "I use ... for ... what do you use?" seems less of a problem.
In both cases though, I can imagine some might think your question close enough to consider closing.
On the other hand, the question is supported by the existence of the "mathematical software" tag. Rarely used, but it must be there for a reason. In a way, it's also the software equivalent of a reference request.
My personal opinion would be that it's a useful question to be answered for those interested in CS, as a "practitioner of computer science", I would like to know of tools specific to my work. I can also see Raphael's point, though I'm leaning the other way I can't give a clear-cut justification of its topicality.