How should I cite a website URL?
Echoing the comments and other answers, citing a website is no different to citing any other resource, such as a book, or a paper. Depending on your favorite text editor and reference manager, you would like to produce bibliographic entries, such as


  ... for the implementation of the prototype, we used the Ruby programming language [23] and ...
  ...
  ...
  Bibliography
  ...
  23. Matsumoto, Yukihiro. Ruby Programming Language. http://www.ruby-lang.org/, 2009.


In BibTeX, there's @misc entry for that. You would use it as follows:

@misc{links/Java,
        author = {{Sun Microsystems Inc.}},
        title = {{J}ava{\texttrademark} {P}latform, {S}tandard {E}dition 6},
        howpublished={\url{http://java.sun.com/}},
        month{jun},
        year = {2006}
}

 @misc{links/xml,
        author = {{W3C}},
        title = {{Extensible Markup Language (XML) 1.0}},
        howpublished = {\url{http://www.w3.org/TR/REC-xml/}},
        publisher = {World Wide Web Consortium},
        year = {2008},
        month = {November}
}


Since websites are a dynamic resource, you should always include the date (year/month) of the last retrieval. 

For the url, the code above would assume \usepackage{url}.

Another technical issue with this is whether your chosen bibliography style would include the URL in the reference, or not. You might want to consult this questions at tex.SE