References that are not literature or qualified sources
As a computer scientist, I often encounter this as well. I have seen three main approaches used, in decreasing order of preference
- Cite the paper about the software, if one exists: academic software is often the subject of papers, and the authors very much appreciate those citations, often explicitly requesting them in the software documentation.
- Cite the software as a miscellaneous reference: most citation styles will have an explicit recommended means for doing so, (e.g., this post on APA software citations)
- The first time the software is mentioned, put a link to the software in a footnote or parentheses.
The earlier ones are better for the authors of the software, but I have sometimes had journals refuse to allow me to give a proper citation.
If a particular piece of software is essential to achieving an end then it is probably best to cite it explicitly, including version number. This makes it possible to reproduce results. However if it is a generic tool then it may not be so important. Operating systems are usually interchangeable for most purposes as are many middleware tools. But specific statistical or mathematical libraries might be more important to name.
However, it is good to at least acknowledge, say in a footnote or acknowledgment section, the creator of any tools you depend on.
However, as an educator, it might also be good for you to over stress citation at least a bit so that students get in the habit of it for their later work.
How you cite it is probably less important than the fact that you do, however.
I'll add to @jakebeal's excellent answer that citing the authors of software packages also gives them the credit they are due. Whether you rely on previous researchers' work in the form of publications or in the form of research software, they ought to get credit in the form of a citation.
We can argue all day long whether citation credit should towards people's job evaluations, but the fact is that it does. If we want to encourage people to make the software that comes out of their research public and available to others (as we do when we require people to publish papers), then we need to make sure that the incentives are so that they will want to make their software available. One way to do this is to ask people to cite the relevant papers/websites/sources whenever they use research software packages.
(This would not apply to commercial packages such as MS Word, Mathematica, etc, since for their authors, the incentive structure is different. Although I would point out that if your research depends on one package specifically -- as opposed to something like MS Word, which you could easily substitute by LibreOffice Writer -- then you probably want to mention and cite that.)