I ask jamawani, and he tells me where the good roads are.
Seriously.

I think his advice is great.
On an early tour, I dd some seat-of-the-pants routing, and found that visitor information centers / chambers of commerce often had county-level maps with back roads on them, and that a little asking around about traffic and shoulder helped *somewhat.* It's pretty rare that non-cyclists can tell what a good biking road *is* but sometimes they can tell what it *isn't* - like they can tell you not to go on a certain road at a certain time of day because that's rush-hour for the mill workers, etc.
For my two overseas trips, I used a combo of Lonely Planet cycling guides and local cycling guides. I've also used a cycle touring guide of Colorado.
Lastly, I generally choose my routes specifically for roads and terrain that I want to ride, rather than particular end points. So my focus starts with interesting, beautiful and safe roads, and the route springs from those, rather than a destination. Sure, sometimes there are some icky transit sections that just must be dealt with, but when you start with a focus on the riding, rather than the start and end, you can end up with a better overall experience.