There's really only one choice: the Karakorum Highway.
Regular buses travel between last Pakistani town on the highway, Sust, and Kashgar. The only caveat is that the highway is subject to closure during the cold season, so it is best to arrange for travel before November. Sust is not a particularly nice place, so if possible try and get tickets before showing up there. If you have to wait a few days before the bus goes, however, just head back down the highway to Passu or Karimabad, which are very nice.
Getting to Sust is easy since the Karakorum plunges down through the mountains to the Punjab, where Rawalpindi and Islamabad are located, so you can start your journey from there by tavelling to Gilgit, which is the largest town in the Northern Areas and a transportation hub. If you are in the Hunza, you'll also want to make for Gilgit, unless you can find transportation directly to Karimabad.
Wherever you find yourself on the highway, there are lots of buses (further south) and minibuses (further north) travelling in both directions. Pre-earthquake, it was possible (if technically forbidden) to enter Azad Kashmir and visit Muzaffarabad, but this is strictly optional.
A note about the bus between Sust and Kashgar: it's a two-day ride and you'll be put in a hotel (likely unheated) for a night in Tashkurgan after passing through Chinese customs. The hotel price should be included in the bus ticket, but you might want to double check that. There's also a "park fee" you have to pay to travel through the last bit of Pakistan. It's very modest.
Currently, the most safe region is Hunza and towards China. Take a NACTO bus from Gilgit city. I don't think there any any issues related to security in the region. Afghanistan and Kashmir are not on the way to China :) The people there live above 2000m altitude, no terrorist can breathe in these regions :). To enjoy and know more be with a local.