XWiki is a WikiWiki clone written in Java that supports many popular features of other Wikis like the Wiki syntax, version control, attachments, security, and searching, but also many advanced features like templates, database and dynamic development using scripting languages (Velocity, Groovy, Ruby, Python, PHP, and more), an extension system and skinability, J2EE scalability, an XML/RPC remote API, statistics, RSS feeds, PDF exporting, WYSIWYG editing, an Office viewer and importer, and a lot more.
Groowiki is a Wiki program and a document management system together. It is a wiki program that utilizes Subversion, Groovy, Velocity, and many more existing products. It lets you edit Wiki pages in a tree structure just like any other wiki, but it also gives you SVN access that makes it very easy to add files to the content. It stores everything in SVN. This way all information is versioned and (optionally) accessible offline, and you can upload your modifications in batches. This is especially useful if you work with large files and the Wiki pages mainly summarize the contents of the documents.
Scripturian is a compact library that makes it very easy to integrate JVM languages (which support JSR-223). It lets you embed "scriptlets" into text documents, in the style of PHP, JSP, and ASP. It also allows boot strap JVM applications using any of the supported languages, which makes it easy to quickly configure and make changes in how your applications start up without re-compilation.