There are, of course, things that cannot be vague enough to be anything but bad science. "The electromagnetic force doesn't work any more!" Well, if the electroweak force suddenly stopped working, we would all die more or less immediately. How do you think your neurons work? How do you think ionic bonds work, for heaven's sake? So you need to actually do the research and find out that building a Faraday cage is what you want rather than the destruction of the universe as we know it--simply saying, "I dunno, it just works that way," is not enough there.
Also, if you have something with problems, listing the problems in character conversation can sometimes get you through. "It took us years to figure out how to deal with the momentum problem," a scientist can say casually, shaking her head at the amount of effort required, or, "The toxicity of the byproduct nearly had us beat," and there you go, you have acknowledged that this is a problem, you have not had to become a Nobel-prize-winning scientist to write your story, on you go. (I mean, if you feel like becoming a Nobel-prize-winning scientist, that's totally fine, and don't let me stop you. I just feel that it shouldn't be a requirement.)
Anybody else have some ideas about writing good handwavium vs. bad fake science? Striking examples in either direction?