Here's how I reached part of my packing method.
1. If I stop somewhere and put my bike down, I'll lean it down on the left side to avoid getting grass and dirt in the drive train. Because of this, the less fragile items go in the left pannier. (The netbook is potentially fragile, but it's packed in the centre of the bag. Also, it has a solid state drive instead of a hard drive, which makes it a bit more durable than other portable computers.)
2. Because summer storms can come up in a hurry, it's a good idea to have the rough weather gear near the top of the clothing bag.
3. I like bears, but I don't want them in the tent with me. Therefore, it's a good idea to keep food and other smelly items separate. The only food I carry is either tinned or dried, but things like toothpaste are always kept in the same pannier, which will be stored outside if bears could be a problem.
4. The front-back balance doesn't mean nearly as much to me as the side to side balance. I've ridden with several front-back load splits and in the end, it doesn't make much difference to me. I know some here will speak highly of having most of the items in front, but it hasn't been a big deal for me at present.
5. Things in the handlebar bag should be things I'll either need to get at quickly or things valuable enough not to lose. If I'm going to take just one bag with me into a store, it will be my handlebar bag, so the most precious items should be in there. Also all bags should be packed so the items that will be needed fastest are easiest to reach.
My list is what has worked for me so far. It's a work in progress and it's subject to change. It's meant to be my guide, but not everyone will want to pack the same way, and that's completely fine.