Botnet, by and large, are responsible either directly or indirectly, for most of the malicious activity on the internet. When it's spam, viruses, drive-by downloaded, rogueware, scareware or all-out DDoS attacks, these large, distributed networks of zombie computers are usually behind it.
Recently a couple of the big ones have been taken down (or at least cut down in size) by the legal manoeuverings of Microsoft and the investigation and arrests of some key players. The Microsoft actions were against the Waledac botnet and the Spanish authorities caught up with some crafty characters responsible for the Mariposa botnet.
straight from the horse's mouth -->Waledac
Panda helps in arrests -->Mariposa