Since they tell you the needs of the website, you can list those down and how the website meets those requirements, which would help in an analysis if the site goes for an upgrade later.
You could record the hierarchy of files, directories, and associated permissions (be it server permissions or whether it is for the management or for the ordinary employee). This would help in maintaining the files.
For PHP scripting you might comment on a config file, if one exists, or even write a data dictionary (i.e. a separate document that lists the variables used on every script and what do they do), though that is probably going overboard.
Easiest would still be writing relevant comments as you code, and giving a commented introduction to the current script at the start.
Of course this is not exhaustive, you might document other things, perhaps even potential bugs/loopholes or any algorithms that you implemented.
