If you were to sit down at any random Windows workstation or home desktop, what would be the most common theme among them? Since even the Microsoft logo changes from version to version, the most prevelant theme among them all is going to be their rate of infection. Some 60% (or more) of machines running Windows that were scanned by the 'Windows Malicious Software Removal Tool' (a standard download as part of Windows updates) were infected by zombie bot trojans, which currently rank as the premiere threat to a Windows PC. Moreso than keyloggers, mass-mailers and plain destructive viruses, bot software is a problem not only because of the damage it can do to the users PC, but the damage it can do to remote PCs as the machine is added to a growing number of PCs used in DDoS attacks.
According to the report, 16 million different bot infections were removed from 5.7 million unique computers. This data may not match up directly with the actual number of infections, considering the number of pirated copies of Windows being used and also the people who do not use automatic updates. Rootkits, too, are a problem, with a 14% infection rate noted by Microsoft, though it is still considered something that hasn't reached "widespread prevalence".