I can only assume they Others/Dharma have folders not only on Jack, Swayer, and Kate, but most if not all of the other Losties. When the episode starts, and Benry sends out the two "scouts," he says he wanted Lists in 3 days. I guess i saw that meaning, they wanted to know WHO survived. Once they found that information out, they began compiling a history of each individual.

As to why they ONLY wanted those 3 people, i have NO idea...still trying to work that one out.