Sites of Japan's Meiji Industrial Revolution by Daniel C-Hazard
I can only speak for the sites in and around Nagasaki, but what I saw was fascinating.
On a sunny December day, I started with a tour of Glover Garden, which offers great views over Nagasaki and has some historic buildings from the early Meiji period, including the listed Glover House and Office.
The highlight of my visit was definitely the boat tour to Hashima Island (Gunkanjima), a truly weird place, different from anything else I have seen so far. I chose Gunkanjima Cruise for the tour and was satisfied with them. Their ferry “Black Diamond” departs from Motohuna pier, located between Nagasaki station and the Youme Town Yumesaito shopping mall. The boat ride offers some nice views of the Mitsubishi Heavy Industries shipyard, crane and dry dock on the Western side of Nagasaki port and the Kosuge Slip Dock on the Eastern side (all part of the WHS). Thanks to calm waters that day, mooring of the boat at Hashima Island was allowed, and although it was prohibited to walk around freely, it was still possible to gain an impression of the site and take some great photos from the southern part of the island. On the way back, the ferry stopped at Takashima Island for half an hour, just enough time for a short stroll.
Further recommended sights in Nagasaki: Atomic Bomb Museum, Peace Park, Fukusai-ji, Ōura Church (part of the WHS “Hidden Christian Sites in the Nagasaki Region”).