It has become common practice to setup "Sinkholes" to capture traffic sent my infected hosts to command and control servers. These Sinkholes are usually established after a malicious domain name has been discovered and registrars agreed to redirect respective NS records to a specific name server configured by the entity operating the Sinkhole. More recently for example Microsoft gained court orders to take over various domain names associated with popular malware.
Once a sinkhole is established, it is possible for the operator of the sinkhole to collect IP addresses from hosts connecting to it. In many cases, a host is only considered "infected" if it transmits a request that indicates it is infected with a specific malware type. A simple DNS lookup or a connection to the server operating on the sinkhole should not suffice and be considered a false positive.
The data collected by sinkholes is typically used for research purposes, and to notify infected users. How well this notification works depends largely on the collaboration between the sinkhole operator and your ISP.
On the other hand, you may want to proactively watch for traffic directed at sinkholes. However, there is no authoritative list of sinkholes. Sinkhole operators try not to advertise the list in order to prevent botnet operators from coding their bots to avoid sinkholes, as well as to avoid revenge DoS attacks against the networks hosting sinkholes. Some ISPs will also operate their own Sinkholes and not direct traffic to "global" sinkholes to ease and accelerate customer notification.
And of course, you can always setup your own sinkhole, which is probably more effective then watching for traffic to existing sinkholes: See Guy's paper for details http://www.sans.org/reading-room/whitepapers/dns/dns-sinkhole-33523
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