After studying the Chicago Manual of Style (especially the references section), I decided on the following format to cite URLs.

There are two cases:

You cite a webpage (URL) only

1. the author of the webpage followed by a period (this is optional because it’s often impossible to determine authors of a webpage)
2. the title of the page (this allows some freedom too if the webpage title is not satisfying) followed by a period
3. the URL in typewriter font (including http:// because some URLs are ftp://)
4. the date when the URL was last checked (month seems sufficient)

An example would be:
“MPI Forum. Message Passing Interface (MPI) Forum Home Page. http://www.mpi-forum.org/ (Dec. 2009)”

Example bibtex:

@misc{mpi-forum,
  author = {{MPI Forum}},
  title = {{Message Passing Interface (MPI) Forum Home Page}},
  howpublished = {{\tt http://www.mpi-forum.org/} (Dec. 2009)}
}

You cite a document which is (only) accessible online

1. the author of the document followed by a period
2. the title of the document followed by a period
3. the URL in typewriter font (including http:// because some URLs are ftp://) preceded by “available at: ”
4. the date when the URL was last checked (month seems sufficient)

An example would be:
“MPI Forum. MPI: A Message-Passing Interface Standard. Version 2.2, September 4th
2009. available at: http://www.mpi-forum.org (Dec. 2009).”

Example bibtex:

@misc{MPI-2.2,
  author={{MPI Forum}},
  title={{\textsf{MPI}: A Message-Passing Interface Standard. Version 2.2}},
  note={available at: \url{http://www.mpi-forum.org} (Dec. 2009)},
  month={September 4th},
  year={2009},
}