MITK git tag <attic/multilabel-2014.03> contains a contribution by Sebastian Ordas which brings support for a multilabel segmentation to MITK.
Further contributions have been done by Jonas Cordes.
Since the original branch diverged heavily form the current MITK master the integration of the multilabel support will be in separate branches. The according files will be moved from the tagged version mentioned above.
First step, is to create a new module which contains the basic data structures, IO classes and the mapper.