Last fall, I completed a trip from Pittsburgh, PA to Charleston, SC. I rode the GAP and C & O to Washington, DC--and I really can't stop raving about the GAP and C & O. If anyone thinks there's a better auto free bicycle route in the country, I'd love to know where it might be.
You have a lot of choices, but I concur with briwasson and cdavey. If you only could choose one section of either the GAP or C & O, I'd ride the GAP from Connellsville to Cumberland. The landscape is beautiful, the towns are friendly, the trail is well maintained, and it felt remote in places. Between Connellsville and Ohiopyle, you ride for ~17 miles without crossing a road, which is a lot for the eastern US. It was a spectacular ride, to say the least.