I was asked to provide my comment as an answer, so here it is. It is yet another way to cite software. However, it requires some effort from the software authors.
I developed an Open Source Web tool for modeling and gathering data when following a certain theory/methodology in software engineering. Here is how you would cite it:
Graziotin, D and Abrahamsson, P 2013. A Web-based modeling tool for the SEMAT Essence theory of software engineering. Journal of Open Research Software 1(1):e4, DOI: http://dx.doi.org/10.5334/jors.ad
This is possible because I opted to publish a software paper in the Journal of Open Research Software. It is a fully Open Access journal. This journal only accepts software papers on open source software for research.
A software paper is a special kind of paper, which describes the software-e.g., what is it about, implementation and architecture, its availability, and its reuse potential. The editorial process works as in any other research venue, and articles are peer-reviewed.
The article processing charges are 25GBP. However, they can be fully waived if you cannot afford them.
What it is nice with this approach is that researchers have an extra motivation to open their software for research: they get a publication for that, plus citations. Additionally, writing a software paper is far easier than writing a methodology paper.
I wrote a review of the journal on my blog. TL;DR; Great experience, go for it.