Nagasaki

Nagasaki is a gorgeous port city with many attractions here are some:

Glover Garden

Daniel Glover was a Scottish merchant of high standing during the time when foreigners were still restricted in Japan. His residence is featured in the drama Ryouma Den and you can tour it for yourself here. The gardens are nice but the actual rooms in the home are a little sparse and the furniture has been assembled from various places and is a little worse for wear. There is however a photo studio where you can borrow clothes sorta from the period and take photos in the garden. There is also a large exhibit of props and costume pieces from the opera Madam Butterfly which took place in the area.

China Town

Not as large as some of the others in Japan and many shops were closed despite it being Golden Week. Lots of souvenir shops and stalls selling amazing pork buns. It's worth visit for dinner.

Peace Park and Memorial Museum

The park is very pretty with fountains and memorial statues from many countries. You can see bottles of water that are left as offerings instead of the usual sake as the Urakami River disappeared in the blast and left the victims lacking water. At the epicenter you can see remains of the Urakami Cathedral (since been rebuilt in another location)and closer to the creek some of the earth from the blast was preserved under glass and you can see pieces of rubble and half melted pottery. At the museum you can see more artifacts of the blast, a replication of the bomb, more portions of the Urakami Cathedral and very moving photos.

Harbour Cruises

Being a port city there are naturally many cruises available from the main harbour. You will see various boats and departure times, most cruises are under an hour and are very reasonably priced. On a clear day you can take great photos. It's recommended you book ahead if you are traveling on a national holiday as they are very popular.

Gunkanjima Island

This was once the most densely populated place on earth, then when the mines closed everyone left virtually overnight and the buildings were left to the mercies of weather and time. It is now accessible by harbour cruise. Once you get off you will be led to three different sites on the island where you can take photos from a safe distance and guides will explain various facts, sadly only in Japanese. It's a great place to take photos and the cruise is extremely popular so book ahead here: http://gunkan-jima.com/