We use freemind not only to organize ideas, but also to organize documents through the links.
It would be nice to extend the search to the linked documents.
So far, the linked documents are of PDF type (95%), plus some text or spreadsheets.
So, extending search to linked PDF would be sufficient.
Could be done may be by plugging to one of this search engines: http://java-source.net/open-source/search-engines , or using the Adobe PDF IFilter.