What is especially interesting to me about these maps is how many of them are actually hierarchical. Many of these maps show complex relationships, but they do so in a flattened way. For example, this diagram (at right) is a radial representation of an organizational map from 1924. On the face of it it looks radically different, but in fact it is a relatively well formed hierarchy with single reporting relationships and only a cursory acknowledgment of horizontal organizational structure in management.
Non-hierarchical, emergent systems are represented well on the site, with this example of a neuron map of a worm brain being really fascinating.
Some of the maps at the site capture complexity in another dimension by creating living maps that change with your focus, like this map of del.icio.us links that you can customize for your own bookmarks.
Finally there are flow chart systems like the ones on world government that seek to understand complex systemic processes