Definitely hit Little Stony Man Cliffs, Hawksbill, Bearfence, and Blackrock Summit in Shenandoah National Park. The waterfalls in Shenandoah are pretty low right now. I would visit Blackwater Falls State Park in West Virginia, sounds like the flow is still doing well over there. Harpers Ferry is an awesome place, make sure you hike up to Maryland Heights for an amazing view of the town. If you wanna head out this far east, the Chesapeake Bay has some cool towns like Chesapeake City and Havre de Grace. Not far from Shenandoah National Park is an amazing hike called Big Schloss, in George Washington National Forest. You can find info about that here http://virginiatrailguide.com/2009/09/21/big-schloss/
If you have a limited amount of time, hit Blackwater Falls, Shenandoah National Park, and Harpers Ferry. Shenandoah could keep you busy for two weeks easily. Theres also some great hiking and views near Blackwater Falls, such as Spruce Knob, Bear Rocks, and Seneca Rocks.
EDIT: If you're visiting in September, the waterfalls should be goin' a little more. In that case, I'd definitely see Doyles River Falls, Whiteoak Canyon, Rose River, and Dark Hollow. Rose River and Dark Hollow can be done in one hike thats much easier than the dedicated Dark Hollow hike which has a very steep ascent coming back up.