A good Wiki (and there is no Java Wiki with these features AFAIK) needs:
- hierarchical structure, usually one level of Areas, with an arbitrary nested Directory structure
- permission system, fine grained, at least Unix-like rwx/ugw for all nodes, including directories
- smart auto link system that supports renaming of documents and directories
- flexible URL schema, e.g. /WikiWord/Links for publishing (marketing) of URLs, and stable identifier URLs (/123.html) for permlinks
- and some more details, like a good default template, XHTML storage, etc.
Have a look at http://www.cowiki.org/ - it's one of the reasons people like the Hibernate.org website.
