Damn it, QB, the Heat Death of the universe is so far away, I'm not sure why you'd need to care about it. And that assumes that the universe is "open" and will never see a "Big Crunch" and then a fresh big bang, running it all in a nice, big cycle. For that matter I actually think witches likely exist because you can't just give thermodynamics the middle finger, so they're some sort of manifestation of entropy within the magical girl system...
Anyway, my two cents on this stuff: it flies in the face of science, and that's never a good thing. I'll concede that it's certainly possible, but highly improbable, to make something which will "run" forever once set in motion. Of course, if it can interact with its environment, that makes things really difficult on the poor perpetual motion machine. And even then, it'd be a curiosity. It can't do any work, because while it'll run forever, if we try to take energy back out of it, it'll stop.
Basically, what other people have said. As for "free" energy, ain't no such thing as a free lunch thanks to conservation laws. If you're getting energy, it has to come from somewhere (other forms of energy, previously done work stored away, matter, the emotions of preteen human girls, whatever).