Besides bigwarp + sciview, I’m aware of:
As far as I can tell, 3d slicer doesn’t do non-linear manual registration. That is, all non-linear registration is automatic - quite a limitation. I’m almost certain that is possible with ec-clem.
Something may possible with paraview, but it’s not meant for this kind of thing, and therefore I expect it would be quite hack. Wouldn’t recommend using it for alignment, unless I’m totally wrong about its capabilities. (That a kitware person “didn’t know what you were talking about” is a good sign its not meant for this purpose )
There are others, probably, and when I think of them, I’ll post here.