I would make a distinction between “scientific software” and “system software”. The latter is commonly used for all sorts of things and could in principle easily be replaced. The former is specifically adapted to produce the results at hand and the results (and only the results, not for example the typesetting of the paper) depend crucially on this software and its correctness.

Examples of the latter are e.g. Linux, libc, systemd etc.: All things used during production of the results, but not aimed at producing such results. The former are e.g. Matlab, the Intel MKL, ALPS, TensorFlow or similar tools and suites. A bug in the MKL may make your results wrong, while a but in the kernel will most likely just crash everything. In my experience, scientific results depend on a handful of software packets in such a way, and adding five-or-so citations to a paper is certainly no big deal and would make reproducing the results much easier.

I have no idea where GNU parallel sits there, it probably depends on how you use it – do you schedule your Monte Carlo runs with it or just rescale pictures for the website? Admittedly, it is a very grey area, but I don’t consider a request for citation unreasonable.