The scourge of spam e-mail will likely never go away, but Microsoft says new data shows that a few targeted anti-botnet operations can reduce malicious e-mail volume by tens of billions of messages per month.

In July 2010, 89.2 billion spam messages were blocked by Microsoft’s Forefront Online Protection for Exchange service, which is used by thousands of enterprise customers. By June 2011, that monthly total was down to 25 billion. Microsoft, in the latest bi-annual Security Intelligence Report (PDF) covering the period ending in June, attributes the drop primarily to the “takedowns of two major botnets: Cutwail, which was shut down in August 2010, and Rustock, which was shut down in March 2011 following a period of dormancy that began in January.”

Consequently, the biggest drops in e-mails blocked occurred in September 2010, when spam dropped to about 65 billion messages, and in January 2011, when it fell under 40 billion. The low point was in May 2011, with about 22 billion, but it ticked up again in June.

Microsoft’s botnet hunters have been busy. Last month, Redmond’s Digital Crimes Unit teamed with Kaspersky Lab to dismantle the Kelihos botnet, which controlled 41,000 computers worldwide and was capable of sending 3.8 billion spam e-mails per day. While Kelihos had the potential to grow, its takedown won’t have the same impact on spam volume as previous operations. The Rustock botnet, with control of 1.3 million zombie computers, was responsible at its height for sending 30 billion spam e-mails a day.

According to Microsoft, 28 percent of blocked spam emails in the first half of 2011 were “advertisements for nonsexual pharmaceutical products,” and 17.2 percent were “nonpharmaceutical product advertisements.” Those pharma ads that aren’t “nonsexual” (we’re guessing mostly V!agra ads) accounted for 3.8 percent.

Microsoft’s security report covers all sorts of vulnerabilities and attacks. In addition to the sophistication of criminal hackers, a lack of user awareness about threats online is a roadblock to creating a safer digital world. According to Microsoft, 340 million PCs are running out-of-date browsers, primarily IE6, IE7 and Firefox 3.6 or older. (Google Chrome automatically updates itself.)

For all the press zero-day exploits receive, they account for less than 0.1 percent of malware detected by Microsoft’s Malicious Software Removal Tool, which runs on more than 600 million PCs, Microsoft said. 3.2 percent of malware was from exploits for which security updates had been available for at least a year, and another 2.4 percent were related to exploits for which an update was available for less than a year. 44.8 percent of malware requires user interaction, and another 43.2 percent comes from malicious software that misuses the AutoRun feature in Windows.

The most commonly observed exploits target vulnerabilities in Java, specifically the Java Runtime Environment, Java Virtual Machine, and Java SE in the Java Development Kit. “Java exploits were responsible for between one-third and one-half of all exploits observed in each of the four most recent quarters,” Microsoft said.

Increased exploitation of a vulnerability in Windows Shell led to a major rise in detected operating system exploits in Q2 2011. Other targets included HTML and JavaScript and Adobe Flash:

Phishing sites also remain a big threat, to users of both financial institutions and social networks. “Phishing sites that targeted financial institutions accounted for an average of 78.3 percent of active phishing sites tracked each month in 1H11 [first half of 2011], compared to just 5.4 percent for social networks,” Microsoft said. The number of popular social networks is smaller than the number of financial sites, but have many frequent users, so phishers can get a bigger bang for their buck by spoofing social networks. “Overall, [phishing] impressions that targeted social networks accounted for 47.8 percent of all impressions in 1H11, followed by those that targeted financial institutions at 35.0 percent,” Microsoft said. A phishing impression is classified as a single instance of a user attempting to visit a known phishing site from Internet Explorer, and being blocked by the browser’s SmartScreen filter.