Fighter Maker - 2D fighting game engine wich difference himself from mugen by the face it doesn’t require any coding programmation; all is done trough an interface, wich make it a very simple engine. Though it doesn’t offer as much possibilities as mugen.
Direct Xion Game - Fighting game engine in developpement wich will propose tools to convert mugen creations. A test version is already available. This engine use the directx 9 technology and seems to be a pretty good alternative for mugen in the future.
Rhakys - Engine in developpement wich goal is to be completely compatible with mugen creations. As soon as this will be a fact, the goal will be to propose fonctionnalities like netplay.
openMugen - Open-Source engine in developpement wich goal is to be fully compatible with mugen.
magEngine - Open-Source engine in developpement wich seems to be on hold at the moment.