Good article by David Dittrich and Sven Dietrich in ;login: magazine which I was able to contribute to by doing a lot of the reverse engineering of the Nugache trojan. The main focus of the article is the evolution of bot networks. Focusing on the details of the command and control structures of various types of bot networks.

Command and Control Structures in Malware: From Handler/Agent to P2P

This is an article that I worked on with Sam stover which covers some of the high level concepts that were introduced by next generation peer-to-peer bot networks. In it we dissect the some of the details of the Nugache and Storm trojans.

Check it out:
Analysis of the Storm and Nugache Trojans: P2P Is Here