Hm....well, I generally go with what's called a "jewelers saw"...at least that's what the guy at the model train store called it....It's about $2 and has sort of looks like a farming sickle, only with a tiny, tiny saw blade attached at the handle, running to the end of the "sickle". they're nice for getting into tight corners, and generally leave a smooth, clean cut (esp on plastics). Some people say to use a dremel tool, but I find them to be boxy, and sort of hard to control but then I'm not the best modeler out there.
Sorry I can't give ya more advice.