Run3 development started in 2009, after experiments with Ogre. Highly inspired by Source, it has open-structure and overall flexibility as basis.
To put it simple, Run3 exists as a run3_r.exe executable file and related DLL's. There is no specific content creation tool for it. You can use any of them.
Specific Run3 tools involve RunEdit(legacy map editor), RunRepresent(model viewer), FacialAnimation(lip sync app), Run3Mat(console until for material batching). Also I use Ogitor for mapping, CaduneTree for procedural trees, CEGUI Editor for the menu GUI, CEGUIMeshViewer for mesh fixing.