We've been to the Pentagon and Shankesville PA but not to Ground Zero yet.
The Pentagon memorial is a challenge to find/get to. There's a huge shopping mall, S of the Pentagon, across I-395, called Pentagon City. If you park there, cross the street heading N, there's a pedestrian tunnel under I-395. Once you exit that, bear left, and there are signs to the memorial. A friend of ours, who was working there on 9/11, said that the loss of life would have been greater except that the portion of the building that was hit, was largely closed for renovation, so many of the offices were vacant. She also said that the portion of the building that was hit is where the Joint Chiefs of Staff offices were normally located.
Shankesville is not very well marked. We were within 3-4 miles of it before we saw our first sign. We were on US30, maybe I-76 has signs? This seems to be presented much better, and more detailed than the Pentagon site. Maybe that's because the UA93 site is now a National Park while the Pentagon remains an active military installation.