i just thought, if moriarty's going to be targetting people sherlock likes.
maybe an interesting way to do it would be molly comes home and jim 'from i.t' is there with toby (this could happen off-screen

)
and molly has to phone sherlock and be like "he's going to kill me if you don't *insert something here*"
normally of course moriarty would stay out of the firing line, but tormenting molly personally might appeal to his sadistic side.

just a little plot thought.