Bibliographic Tools (e.g. LaTeX/BibTeX)
One of the frustrations of computing research is the lack of standard
biliographic formats - each professional organization (e.g. IEEE, ACM, SPIE) and often even individual conferences will use different citation and bibliographic entry styles. Fortunately, if you use LaTeX to create your paper, then publication venues often provide bibtex files that can automate citation and bibliography style.
Make use of bibliography database programs, so that you can easily collect, select, organize, and annotate your references. Most modern systems, such as BibDesk allow you to save the .pdf with the .bib entry, and even mark-up the .pdf file, a very useful feature. There are many systems for organizing paper databases; a short list of systems that I know of include: EndNote, Mendeley, Zotero, and JabRef.
Personally I find that for each paper I write, I need to copy entries from my bibtex bibliography database into a separate file, as different styles use different fields. Further, I find that the formatting and amount of information provided by .bib databases online differs dramatically, and so there is always some editing of the bibliography entries that is needed. Carefully editing your bibliography is a sign of respect to the journal/conference, and more importantly your readers, who need accurate and complete information if they choose to find or quickly scan the references cited in your paper.
Note that using URL's for references is unacceptable when a proper paper citation is available.
If you must
use a URL, accompany the link with the name of the author(s) of the
document, document title
and creation/posting date of the web page.