From Nigel.
Your recollection is correct, I did indeed recommend DokuWiki, for several reasons. As you recalled, I commend the quality of the PHP code itself as worthy of study.
Another primary quality of Doku is that the underlying backing storage is plain text files in the host webserver, which you can copy and move around to easily backup or replicate your wiki instances; other Wiki software (most notably MediaWiki) tends to use a database behind the scenes, which complicates things immensely.
[ I set up a Doku installation internal to the Symantec Auckland site for our internal needs in about 2004, and spent a lot of time expanding and improving it, and it has served us well. ]
Yes, there are Wiki standards, of sorts. These are really more along the lines of consensus about things like how to refer between Wikis, but there is one very important effort which deserves special note. Ward Cunningham, creator of the original Wiki concept and software, put quite some time and effort into trying to get folks to agree on a common syntax for Wikis since there had been an explosion of violently incompatible syntaxes expanding on his original design.
The result is at
http://www.wikicreole.org/ - as with the syntax design of DokuWiki, that consensus syntax is heavily influenced by, but slightly different to, John Gruber's syntax for web publishing, Markdown -
http://daringfireball.net/projects/markdown/ (another piece of code that's worth your time to study & understand).
Although Doku isn't the same as Creole, it's close, and Doku's extra features over and above Creole are pretty powerful.
One other Wiki of practical note is Trac - see
http://trac.edgewall.org/ - not because it's a Wiki as much as it integrates one with a front end to Subversion along with a simple bug-tracking tool.
I wouldn't recommend you install or use Trac, but it's good to be aware of it since that particular package of source control + wiki + bug tracking is something that you will want to get used to if you're interested at all in writing code. Trac isn't anything particularly special compared to hosted environments like Google Code -
http://code.google.com - but it's installable privately and plenty of people use it instead of hosted services.
- Nigel