The KmWiki WikiClone supports in-place editing of diagrams using a JavaHotDraw-derived widget, and objects in the diagram can link to pages. This is pretty cool, but quite complicated and not necessarily terribly useful.
OriginalWiki just supports links to documents, but doesn't give people a way to upload: they have to have their own web server, which makes things difficult in some environments.
It would be nice to let people upload multiple files and replace them later.