I've just released a free application which converts Stack Exchange data dumps to GraphML.
This allows you to analyze the Stack Exchange data using tools like R/igraph and Gephi.
It is interesting to compare Stack Overflow with this analysis of the Java Developer Forum, which is considerably smaller.
The Stack Overflow data is large enough that Gephi struggles with it -- but igraph in R works fine.
I'm open to suggestions for improving the tool, but I'm doing this in my spare time, so pull requests are the preferred form of "suggestion."