As I'm using PhpWiki for several years now and think it has a very promising codebase under its hood, I also understand that it's not widely popular for several reasons. First the standard skin doesn't look that fancy like, say WordPress. For me that was always the least important thing, because I've always created my own templates. But I'm sure it's clever marketing. Second, WordPress is optimized as an out-of-the-box blog with Semantics and SEO in mind. I know PhpWiki has all of this too (see 
Tao of Mac), but it's implementation is more rudimentary. In my opinion most PhpWikiPlugins have just a certain showcase character and you'll have to adjust them very much to your needs - but hey, please prove me wrong!
But on the other hand that's PhpWiki's big plus: Flexibility. I think PhpWiki comes with a terrific core and let's you extend it. It goes that far, that I would say PhpWiki is not just only a Wiki but has the potential being a basis for some kind of RapidWikiApplicationDevelopmentFramework.