I work on Federated Wiki where my community has asked for more graph support. I've provided both graphs of wiki and graphs in wiki.

http://ward.asia.wiki.org/search-index-downloads.html
http://ward.asia.wiki.org/about-graph-plugin.html

I've found that federated wiki and object-oriented programs complicate graph representation due to late binding of links and calls. I've had more success building large graphs of metadata which I have described in the context of Domain Driven Design.

http://ddd.ward.wiki.org

All of the Neo4j folks I have met have been amazingly helpful in this journey starting with Michael Hunger.