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.