Visual Complexity is a site that brings together many different instances of the mapping of complex systems. The maps range from Biology to Social Networks. Each individual project is distinct but all attempt to visualize these complex networks which are nearly beyond comprehension, by definition. The result is often beautiful and reliably interesting.
One mapping project which I find particularly interesting is BlogPulse's mapping of liberal and conservative blogs around the 2004 elections. I linked to BlogPulse a few days ago. This project gives a clear perspective on a limited set if interactions taking place in a starkly deliniated section of the blog-network. Yet is it reductive to try to draw conclusions about an emergent network by analyzing a small portion of it?

"In this paper, the authors studied the linking patterns and discussion topics of political bloggers. The goal was to measure the degree of interaction between liberal and conservative blogs, and to uncover any differences in the structure of the two communities. Specifically, they analyzed the posts of 40 "A-list" blogs over the period of two months preceding the U.S. Presidential Election of 2004, to study how often they referred to one another and to quantify the overlap in the topics they discussed, both within the liberal and conservative communities, and also across communities."