In a paper entitled "Visualizing Social Bookmarks", Joris Klerkx and Erik Duval describe how it's often hard in most social bookmarking tools to discover implicit structures between tags, users and bookmarks. This is mostly due to the flat nature of tags, and an intrinsic trait of folksonomy in opposition to traditional hierarchical structures.
In an effort to solve this problem, the authors designed a system that "attempts to visualize these structures, so that end users can explore the social bookmarks in a playful, efficient and flexible way." In this work, a cluster map visualization application is customized to enable users to explore social bookmarks in the del.icio.us system. The design of the application aims to automatically identify tag and community structures, and visualizes these structures in order to increase the users' awareness of them.
You can also read the paper (pdf) here.