The Linkexplorer organizes tagging by defining various relations between tags. This is similar to the approach used by BibSonomy. But there are different types of named relations (eg part-of, related-to, etc). This greatly helps to organize tags. However, I think tagging is quite uncontrolled and it will be difficult to have usable visualizations of relations between huge amounts of tags. Further, I am not sure if it should be called structured tagging. Some people use the term “structured tagging” to refer to structured metadata.
Linkexplorer.net – experimental structured tagging