Generally, you should not be citing websites. According to the author instructions for the journal Ecology (as well as all publications from the Ecological Association of America), "The Literature Cited section of a paper may refer only to permanently archived material...Because Internet sources typically have a short half-life, they may not be included in Literature Cited sections unless there is reasonable evidence of permanency (e.g., Ecological Archives). As a general rule, any publication that has an ISSN or ISBN is acceptable, but should be referenced by name (the URL may be added, but is not essential)."
These instructions refer to web sites, not journals that are available on the web (i.e., it is acceptable to cite the journals you find through the Library databases).
Last name, First initial. Second initial., First initial. Second initial. Last name, and First initial. Second initial. Last name. Date.
Title of webpage. Sponsoring organization. web address
Example 1:
Simpson, G.L. 2005. Cocorresp:co-correspondence analysis ordination methods 0.1-3. R package.
http://cran.r-project.org/src/contrib/PACKAGES.html
Example 2:
Van Gils, J. A., T. Piersma, A. Dekinga, B. Spaans, and C. Kraan. 2006a. Shellfish-dredging pushes a flexible avian top predator
out of a protected marine ecosystem. PLoS Biology 4:2399–2404.
