The evolution of molecular markers -: just a matter of fashion?

In less than half a century, molecular markers have totally changed our view of nature, and in the process they have evolved themselves. However, all of the molecular methods developed over the years to detect variation do so in one of only three conceptually different classes of marker: protein variants (allozymes), DNA sequence polymorphism and DNA repeat variation. The latest techniques promise to provide cheap, high-throughput methods for genotyping existing markers, but might other traditional approaches offer better value for some applications?