Book your passage. Although Nanjing does have a local airport--Nanjing Lukou International Airport--it will be cheaper in the end to take a train from nearby Shanghai. High-speed trains from Shanghai can cover the few hundred kilometers in as little as 2 hours, whereas local trains may take up to 6. High-speed trains are known as "D trains."
Make your first stop at the Nanjing Massacre Memorial Hall, which commemorates the 1937 massacre of 300 thousand Chinese by the Japanese army. The memorial site includes not just memorials and monuments, but a preserved mass grave of approximately 10 thousand victims. The hall, meanwhile, can take several hours to go through--the evidence and history is extensive.
Decompress with other local attractions. The Nanjing Zoo is actually a charming green space, and a good deal more cheerful than the notoriously depressing Beijing Zoo. Also available are the Nanjing Museum, ideal for a rainy day, and the Presidential Palace.
Take a trip not just to Confucius Temple--although the temple itself deserves a visit--but also to the surrounding area, which is rife with shops selling everything from silk cheogsams to high-quality chopsticks. This area can be jam-packed with tourists and locals, and at night can light up like a mini-Vegas. Remember that heavy bartering is the norm in China.
Head up to Purple Mountain. This sizable mountain contains 9 separate parks, in addition to the Memorial for Sun Yat Sen, the father of modern China, and the Xiaoling Tomb. A Purple Mountain Pass, granting access to all 9 parks, can be obtained for 100 RMB.