I found this to be a really interesting (and really well-done paper): http://www.ieee-security.org/TC/SP2013/papers/4977a080.pdf
ABSTRACT: Tor is the most popular volunteer-based anonymity network consisting of over 3000 volunteer-operated relays. Apart from making connections to servers hard to trace to their origin it can also provide receiver privacy for Internet services through a feature called “hidden services”. In this paper we expose flaws both in the design and implementation of Tor’s hidden services that allow an attacker to measure the popularity of arbitrary hidden services, take down hidden services and deanonymize hidden services. We give a practical evaluation of our techniques by studying: (1) a recent case of a botnet using Tor hidden services for command and control channels; (2) Silk Road, a hidden service used to sell drugs and other contraband; (3) the hidden service of the DuckDuckGo search engine. NK
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