After several days of searching for a memory leak we've found out that the following Python code causes the memory leak:

scene.GetNodesByClass("vtkMRMLScalarVolumeNode").GetNumberOfItems() > 1

Even if we save the GetNodesByClass output into a variable and then call Delete() or UnRegister, the leak is still there.

The problem is that in vtkMRMLScene::GetNodesByClass a new vtkCollection object is created, which should be deleted by the caller. However, this is counter-intuitive (if vtkMRMLScene created the vtkCollection object then vtkMRMLScene should be responsible for the deletion as well) and very error-prone (as our example showed it).

To avoid such issues, the signature of
vtkCollection vtkMRMLScene::GetNodesByClass(const char className)
should be changed to
void vtkMRMLScene::GetNodesByClass(vtkCollection nodes, const char className)
Maybe for some time the old implementation could be kept, but whenever it's called a deprecation warning should be added to the log.

I've reviewed the full Slicer code base and found that two other classes has the same issue. The complete list of methods that should be fixed:

vtkCollection vtkMRMLScene::GetNodesByClass(const char className)
vtkCollection vtkMRMLScene::GetNodesByName(const char name)
vtkCollection vtkMRMLScene::GetNodesByClassByName(const char className, const char name)
vtkCollection vtkMRMLScene::GetReferencedNodes(vtkMRMLNode *node)

vtkCollection vtkMRMLLayoutLogic::GetViewsFromLayout(vtkXMLDataElement root)

vtkCollection vtkEventBroker::GetObservationsForSubject ( vtkObject subject )
vtkCollection vtkEventBroker::GetObservationsForObserver ( vtkObject observer )
vtkCollection vtkEventBroker::GetObservationsForCallback ( vtkCallbackCommand callback )