Those apps, launched when the user is Facebooking, often require that the user grant extended permission for them to perform their routines, and therein lies the danger.
Because so many users of Facebook are so comfortable -- sanguine, really -- with the social network and its ever-growing array of features (everything from games to which-movie-star-are-you to multi-network posting tools and more), granting permission is often given no more attention that it takes to deliver a mouse-click that gives the go-ahead. No thought involved.
And that's where proper social networking practices at work come in. We've talked here a lot about the business benefits of social networks.
But unless your Facebooking (or other social networking) employees are carefully instructed in what actions are (posting marketing materials on your business's Wall, for example) and aren't (launching apps or posting private information, say) appropriate for business use, it's all too easy for the dream of growing business by networking to become a nightmare of malware infection or worse.