I suppose the easiest way would be to use the \newcommand command in LaTeX.
Put something like this before your \begin{document}:
\newcommand{\jquerynote}{\footnote{\url{http://jquery.com}}~}
Use it as follows.
We used JQuery\jquerynote to build the user interface.
If you want to change the reference to a citation or another format, you can replace the contents of the \newcommand
As far as to "What is the best way to cite a website URL?" the answer generally is that there isn't a standard. Personally, I use web sites as a citation if it contributes some kind of important intellectual argument to the paper. If I use web sites as a footnote, it's because it has to do with some kind of tool I used and is there simply to inform the user that I used Tool XYZ.
Using your example, if I said in my paper, "We used the Google search engine to identify evidence of bias in search engine results" I'd probably put that as a footnote, whereas if I said, "Company web sites from Google, Microsoft, and Apple about employment all state that having fun at work is important" may be citations.
(I should finally note that this is a personal convention rather than anything spelled out in a styleguide, but maybe it helps you?).