You already have the first step: a starting point, ending point, and a set of destinations along the way. Given those desired destinations, I first try to piece together existing routes. For example, peruse ACA routes or crazyguy trip reports, and see if you can connect your destinations using those existing routes.

When that fails (or, if you just want to go off the beaten path), my #1 resource is Google Maps. My approach is to plan 3 or 4 different routes on Google Maps. These were "high-level" routes -- I didn't account for elevation changes, traffic, wind, camping spots, and so on. I just picked routes that hit my destinations and seemed reasonable. Then, for each route, I did some research to determine how feasible the route was. My research included these steps:

• I translated each route into Google Earth to get an elevation profile. You can also use ridewithgps, gmap-pedometer, and a few other sites for this purpose. My current favorite site is ridewithgps. On each elevation profile, I paid close attention to the %grade of each road -- anything above 10% is too steep for me on a loaded touring bike (unless I'm really looking for a workout, or willing to walk).
• I marked all the towns along each route. These are potential resupply points.
• I marked all feasible camping spots along each route. My order of preference is usually USFS campgrounds, State Park campgrounds, BLM campgrounds, and lastly RV parks. You can find USFS campground sites on http://www.recreation.gov and http://www.fs.fed.us/, you can find State Parks via the state's website, and you can find RV parks via Google. For some areas of the US, there are a few mashup websites that combine all of these campgrounds into a single map -- you can find these mashups via Google searches.
• I researched traffic and weather conditions for each route. Most (all?) states publish traffic data for their major highways, however I found that trip reports are actually the best resource for traffic conditions, since they describe traffic from the rider's perspective. Note that you should read trip reports written by local riders, not just tourers -- these reports will often suggest alternate routes that are well travelled by locals. If for some reason you cannot find any trip report for a route you want to take, you can use Google Street View to get a glimpse of the road conditions, or just post a question here.

After the above steps, I had 3 or 4 routes each annotated with elevations, resupply points, campgrounds, and traffic info, and given all this data I picked the route that seemed the most interesting, but within my abilities.

The above approach worked for me, for a grand total of one bike tour I'm sure more experienced riders will have more thoughts.

Hope this helps.