Resources: we used the Lonely Planet, which was helpful for activities but not for food. The tourist office had a decent map with the tram stops and sites in English. Though out of date, a website for exchange students in Isahaya might be useful for some: http://spot.pcc.edu/~jsparks/ESOLClassLinks/Isahaya/IsahayaGuide.htm
Getting around: Nagasaki has an easy and charming electric tram system. You get on, no need for a ticket, and go anywhere on that line for 100Y. Transfers are only available at one stop in the shopping district (Hamanomachi). The ferry terminal is at Dejima station. From there one can buy tickets to several coastal islands including Ioujima. The tourist info office is across the street from the train
station via the pedestrian overhead walkways - take the path towards the drab office building and you're there.Where to stay: there are several chain business hotels in central Nagasaki. We ended up at Comfort Hotel for approx 8000Y a night. This included a good breakfast buffet comprised of an array of breads and toaster capability, boiled eggs, 5 types of onigiri, mini-salads, mini-fruit slices, yogurt, 2 kinds of cereal, milk, an espresso machine, and a drink machine with tea and orange juice.
What to eat: There are lots of restaurants in Hamanomachi (the shopping arcade area), Chinatown, Shianbashi at night. We had lunch at a place with "Farm to Table" written out front. It stands behind the Kanko-dori tram stop. For 980Y and 1200Y we had the pasta of the day set and the daily set. Both came with a salad with mustard seed dressing . The pasta was a veggie white wine cream sauce, and quite nice. The daily set was a slice of Japanese style meatloaf topped with roasted tomatoes, with veggies on the side drizzled in orange sauce and pesto. Dessert and coffee were included but not memorable. We dined at Nanak, an Indian restaurant which also has a branch in Fukuoka, and maybe other places. We got a 2-person set for 3800Y which was more food than one should eat in a day. It included two salads with spicy dressing, a large plate of naan, a beautiful spinach curry, a decent eggplant tomato curry, and an excessively buttery biriyani. The next day, we had champon (the local ramen with seafood) and a mushroom+rice dish at a Chinese restaurant located on a small street that heads diagonally off the extension of Kanko-dori by the Prefectural office. This place had no English menu or English-
speaking waitstaff, but the food was lovely enough to just point-and-shoot. That night, we dined on the same street in a dining bar just up the hill from the Chinese place. The proprietress had a sign out front with lovely pictures of spring rolls. Again, no English menu, although the server helped translate the menu. We had yummy stir-fried chili squid, veggies with korean bean paste dipping sauce, fried fish cakes, and daikon salad, among other things. Dishes were 300-700Y for small portions to share, and beers were 450Y.What to do: Nagasaki is a compact, mellow, strollable city. It doesn't have any "unmissable" attractions, which is part of the fun. It is just a workaday midsized Japanese city which happens to boast some very interesting distant and recent history. Interesting areas include Urakami - the suburb at the hypocenter of the atomic explosion, with its memorial parks, rebuilt cathedral, and Atomic Bomb Museum, Teramachi (Temple Row) - a path in the foothills lined with temples, shrines, and cemeteries, notably Sofukuji and Kofukuji (200-300Y admission each), and the shopping & nightlife zone of Hamanomachi and Shianbashi. The temple row area is slightly posh, with a smattering of attractive cafes and restaurants, of which we did not partake. We also did not
visit the restored residences of Meiji-era foreigners, but surely this is also worthwhile. The waterfront is unfortunately industrial in Nagasaki, with the exception of a seaside park that hosts football games on the weekends, and the unappealing Dejima development. The highlight of Nagasaki was a day trip to Ioujima. For 980Y, you get a round trip ticket for the 20 minute ferry ride to the island, and admission to the seaside onsen. Tickets may be purchased at the fancy counter in the ferry terminal. The walk from the ferry terminal to the resort is about 5 minutes. No need to wait in line in the lobby, you just follow the 
signs to the onsen, see the nice lady at the counter to trade in the onsen ticket for a towel and a return ferry ticket, and then sex segregate. There are 4 indoor pools, all slightly different temperatures. The outdoor space is lovely with a view over the sea at back on Nagasaki harbour. The women and men's areas both have two large soaking pools, and three metal cauldron baths large enough to seat one medium sized person. Unlike many other Japanese onsen, the water temperature was very comfortable, not too hot. The women's area has a hot stone surface with a log pillow that sits at approx a 20 degree angle and hot water trickles down the rock surface - beautiful for sunning yourself. Ioujima also boasts a cathedral and a beach, both of which might be explored by bike or scooter, but we spent all our time at the onsen.
