What software to cite in a manuscript, and how?
After some thought on the matter, my own approach in my next manuscript will probably go like this:


Which: To choose which software to cite, I would try to answer the following questions:


Is there a scientific article that can be cited and are the authors of the software asking to be cited? 
Was this specific software relevant to the results of the manuscript? If there are plenty of alternatives to the software and you use it merely because you knew it, this is probably not a reason to cite it. But if I used and profited from the specific features of a software, then it is probably worth citing it.
Do I explicitly want to give credits to the software? Maybe I found the software very good to use and I want to tell other scientists to use it, then I would cite it.

How: If there is a scientific article, I cite it in the classical way. However, I would also cite a URL of the software, as this makes it significantly easier for a reader to find the software. Otherwise, cite the URL. Citing the manual doesn't make sense to me, the only reason to do so would be to give explicit credits to an author.
Where: If I can cite a software in the course of the text, I do so, otherwise, I would make an appropriate paragraph in the Introduction or Acknowledgements.