Few ideas from the two times I've been to Nanjing.

Massacre Memorial: Plan at least 2 hours here. We only planned 1.5 and wished we had more time. The grounds are huge and you can check out all the sights, but the actual museum is actually very very large and has LOTS of very good displays and info. More than what appears from the outside.

Purple Mountain: If the crowds are getting to you, this place is pretty nice and quiet. There isn't a lot to do up top, and when I was there in July the Astronomy place was closed (half way up the mountain). You can certainly do some hiking and sightseeing, but don't set your expectations high for things to see or do. But if you're looking for a place to escape crowds, get outside, and catch some good city views it's a perfect place to go.

Zhonghua Gate: Pretty neat, you can see this entire place in an hour or less. Inside the tall structure there are some neat displays you can pass time. If it's hot, the temps in here are a lot cooler too. I was there when it was close to 100.

River Bridge: Far off and somewhat hard to get to. We were worried about catching a cab back, but were able to find one in about 10 min (you can take a bus too). Park wasn't that interesting though it was large, and the actual bridge was somewhat of a disappointment. You pay something like 10 RMB to get to the street level, and another 5 level to walk the stairs to the second level. If you're rushed for time, I'd skip this unless you like river views. Nothing super impressive.

Fuzi Miao: definitely worth checking out. I'd go at night as it's more lively then and more fun. Catch a boat ride, or grab a bite to eat at the famous Nanjing Dim Sum style restaurant. Also, tons of cheap goods you can buy here and bargain for (clothes, DVDs, pets, you name it they have it).