After receiving some reports of mail incorrectly flagged as spam or phishing attempts, Google has confirmed that the problem with their malware list also caused mail to Gmail accounts to be marked as spam:
This morning there was a problem with the implementation of Google’s malware filters. Gmail’s spam engine uses those filters (among hundreds of other signals) to help protect our users from malware, and so between 6:00 a.m. PST and 8:00 a.m. PST, we mistakenly sent some legitimate mail to people’s spam folders.
Fortunately, most messages have been restored. Apparently Google’s spamfilters are more likely to classify a message as unwanted if it includes a link to a know malware site. It only took them two days to restore the incorrectly classified messages; which makes me wonder whether they already have a mechanism to apply updated classification rules to unread mail. That would make sense to me, and given Google’s massive server farms they probably have the CPU power to do this.