The sources in the reference list generally validate particular claims that are made in the body of the text. Some style manuals support putting software resources in the reflist, like APA, some don't, like Chicago.
In APA (6th ed., section 7.08), the reference should look something like:
Free Software Foundation (2007). Bash (3.2.48) [Unix shell program]. Retrieved from
Here, the FSF is identified as the rights holder, and the version used for the results in the paper is identified, and the URL for downloading that version of Bash is given. This form is appropriate when the software is used to generate results that are the source for claims in the paper.
If you want to cite a particular claim about Bash that comes, say, from a web page, then cite that web page specifically, with a literal quote. If you just generally want to identify Bash through a webpage, then use a footnote or endnote, and link to the project webpage at http://www.gnu.org/software/bash/. Don't put anything in the reflist in this case.