I guess this is a late post, but I use both dokuwiki and pmwiki and like them both very much.

I think the biggest difference is in how many users will use your wiki. Dokuwiki serves my purposes better as a multiuser wiki with a namespace-based permissions system. Pmwiki, I think, is better as a wiki for personal use, or small projects. Though I think that Pmwiki has more robust options for customizing layout than Dokuwiki, if that's what you want.

Dokuwiki also has a neat internal filesystem; the namespaces correspond to folders, and each wikipage to an individual text file. The wikisyntax for Doku is designed especially so that the text files are more human-readable, so there are some big differences between other wikis in syntax (mostly in headers and bullets).

Anyway, all this to say that the choice really depends more on what you want to do with your wiki than anything.

Sally