Our primary tools continue to be opensource R&D codes, so we have picked OpenFOAM and ElmerFEM. The benefit of picking these codes is that we have access to the underlying numerical methods, and can adapt code to suit our purposes. They are also really well supported, and have small communities of scientists extending their applications all the time.
For more information visit OpenFOAM's website
Dam Break: DamBreak.avi, DamBreak.wmv
For more information visit ElmerFEM's website
Mistrangelo, Simulation of MHD flows: electric potential formulation
Panchal, Study of liquid metal MHD flows using OpenFOAM
Mas de les Valls, OpenFOAM capabilities for MHD simulation under nuclear fusion technology conditions