Among the clues, according to Sioux Falls' Argus Leader: The car "was in third gear, with the keys in the ignition and the lights on. One tire was damaged. ... Miller's purse was found, Jackley said. Inside it was her license, notes from classmates and photographs." Source: NPR (blog) - by Mark Memmott
Read more about the details of the cold-case and how the girls were found.