Zwiki is a GPL'd Wiki Wiki Clone based on the powerful Zope Application Server (Zope), from which it gains a great deal of leverage. Zwiki is flexible and has some unique capabilities, combined into a reasonably intuitive whole. It combines well with other Zope add-ons such as Plo Ne. The polish and documentation is improving. We'd welcome your help.
Zope is cross platform and easy to install or find free hosting for; if you can get over the Zope requirement, in my biased opinion you should take a close look at Zwiki. (And if it's not right for you, I'd love to hear why - thanks!)
Start here
Optional page hierarchy: organize pages as an outline
see Page Hierarchy for discussion of this.
Wiki can act as a mail list, or integrate with a real one
Optional dynamic pages (sandboxed server-side code)
Simple issue tracking
Latex support
See also Mojo Mojo and a link to a comparison using the Wiki Matrix: www.wikimatrix.org 
See original on c2.com