Amelia Bones was a very powerful witch, as well as being in the "Fudge you're not necessarily right" camp in OotP (being a strong voice speaking out for Harry during the trial). She was very active in the anti-Voldemort movement, although not necessarily in the Order.
I don't think that it took anything quote "special" about people in order to be killed, as long as they were anti-Voldie. We just know that what she did against his second coming must've had a greater impact if Voldemort took her out personally.
As evil as Voldermort was, I don't beleive that he would him self commit a murder if the victim was not worthy. Remember that he cherished him self beyond any limit, the dirty job to extreminate those in the anti Voldermort movement was left to his death eaters, that would do anything just to prove worthy of his appreciation, but he appreciated no one.
So Amelia Bones, we come again to this, meant mose likely a big obstacle to his plans or engagements, additional fact was her capability what only increased the threat. Remember again, she beleived Dumbledore that Voldermort is back, so I don't beleive that she seat down watching the World pass by.
She was considered "the greatest witch of her age", which suggests that she's superior to the likes of Bellatrix Lestrange and the Malfoys. Lord Voldemort probably didn't kill her because she was an authoritative threat to him but because she was a powerful and influential witch who might kick the shit out of any two-bit lackey that he sent after her.