For some months now, Google has been trying to detect malware on the sites in its search results. If it thinks a site is affected, it displays a note to that effect on the results page, and tries to contact the site operator so that they can take action.
Google don't say how they detect malware, but it's unlikely to involve WoT in my opinion. WoT aims to rate a site's reputation among a community of users. It's not specifically concerned with malware, which is often beyond the immediate control of the site's operators.
By all means use WoT if you plan to have dealings with a site (if you are thinking of buying a product from them, for example), but, when it comes to SEO, there are more important things to worry about.