http://c2.com/cgi/wikibase
http://www.emacswiki.org/cw?TooManyWikiEngines
There's tons of different WikiEngines http://wikifeatures.wiki.taoriver.net/moin.cgi/WikiEngine (or WikiClones http://www.emacswiki.org/cgi-bin/latin-1.pl?url=http://www.usemod.com/cgi-bin/mb.pl?WikiClone) out there. This provides a vibrant diversity of ideas, but it also means that the sum total of wiki developer effort is split into 1000 pieces.
One aspect of the problem is that in order to try out a few new features, often a developer simply forks a WikiEngine. The different wiki engines are like lots of small tidepools, each of them with a few unique features, most features being stuck to their WikiEngine.
Similarly, it is hard for a new feature or a new WikiEngine to be adopted by many wiki communities; wiki communities are "stuck" with their current wiki engine, because it is hard to move the content to a new one.
My personal effort to improve the situation is not to try and get convince people to stop forking wikis, but instead to create tools which make the situation more fluid. Tools to allow new features to flow more easily from one WikiEngine to another. And to allow WikiEngines to fluidly flow into one another. Another word for "fluidity" here is probably "interoperability".
http://www.usemod.com/cgi-bin/mb.pl?action=browse&id=WikiEngine&oldid=WikiClone
The historical and some might claim canonical term is actually "WikiClone", a term originally coined to describe sites built with software imitating the WikiWiki idea before WikiEngines were common. FridemarPache has since rebuilt the entire ontology at WikiWiki to be more consistent and clear; i.e. to differentiate the software at the back end of a wiki from each separate instantiation of a wiki - whereas before it could have been said that, for example, "MeatballWiki is a WikiClone", it would now be said that (obviously) "MeatballWiki is a wiki".
We support that naming system here, although people often shortcut to just saying "a wiki" rather than "a WikiEngine". "A WikiForum" is also available as a synonym to "a wiki", although it is infrequently used. For an exhaustive, or perhaps exhausting, summary of the meanings of "wiki", see WhatIsaWiki.
There are many many wiki clones (too many? see CommunityWiki:TooManyWikiEngines) out there. If you want the original, go to
http://c2.com/cgi/wikibase
Some good wiki software. (There are many more. See Wiki:WikiWikiClones and Wiki:WikiEngines.)
PhpWiki (PHP) Probably the most faithful to the original wiki of this list.
TwikiClone (Perl) Probably the most divergent, but powerful.
MoinMoin (Python) Very, very, very popular. Possibly the most popular. Being implemented in Python this is easy to extend - even if you never heard of Python before.
PikiePikie (Python) Functions very nicely as a "WikiLog."
ZwikiClone (Zope) If you like Zope.
WikkiTikkiTavi (PHP) If you like UseModWiki in PHP + its own nice features
LogiLogi (PHP) Like Tavi + Sections and Multilanguage
WoDev (WebObjects?) WebObjects? based wiki site
Chiki (WebDav) If you like easy ;)
[Kwiki] (Perl) easy to install, modular
WikkaWiki (PHP)
A lightweight/easily customizable WikiEngine forked from the glorious WakkaWiki?
UseModWiki (Perl)
If Perl is your friend. This site runs UseModWiki Perl need not be your friend. If you don't have your own web server, and rely instead on free or inexpensive commercial servers, they are far more likely to support Perl than many of these other languages, alas.
My favourite is UseModWiki (for obvious reasons), but that's because it bests suits my needs for MeatballWiki, and if it doesn't, I can upgrade it so it will. It's also very configurable, so it also serves about a billion other people's needs, right up to the largest wiki on earth, WikiPedia, if you can call Wikipedia a wiki. (and you discount EverythingTwo).
OddMuse (a UseMod descendant) can use UTF-8 (UseMod cannot, there is a "forbidden byte") — AlexSchroeder (No longer the case in UseMod v1.0) — ChuckAdams.