I wrote some code transforming an arbitrary list of data nodes with a matrix:

std::set<mitk::DataNode::Pointer>::iterator i;
for(i = myList.begin(); i != myList.end(); ++i)
{
  (*i)->GetData()->GetGeometry()->Compose(matrix);
  (*i)->GetData()->Modified();
}

This works fine for all three basic data types (surface, image, pointset). If you save the data, however, only images and surfaces are saved as "transformed" and pointsets remain and their previous position. This behavior is wrong and inconsistent.