I would appreciate if somebody could get back to me regarding the MediaWiki and J2EE applications integration. The idea is to use MediaWiki for the presentation (end-user interface) layer and documentation management, and from the same MediaWiki-based presentation layer communicate with a J2EE application that provides enterprise information management (i.e., product life cycle management, project management, stakeholder and organization management, CRM, etc.).
Goran,
Take a look at the External Data extension:
http://www.mediawiki.org/wiki/Extension:External_Data
It may do what you want. I've been planning on adding other protocols, such as SOAP or XMLRPC, to it.
Otherwise, you could probably do iframes or write your own extension.
V/r,
Ryan Lane