When I come to Tokyo I sometimes stay in the urban hubs like Shinjuku or Ueno, but I can then get worn down by the crowds, especially late at night when the club and bar touts are active. So with the subway running until after midnight, it's often little burden to stay in a less central, more low-key neighbourhood, and it also allows me to get a taste of everyday Japanese life, away from the touristy sights. So on my last trip I chose Hostel Fuji, close to Shinjuku on the subway, far away in terms of atmosphere.
It's a small place, with just two dorms, a larger one with twelve capsules, and a smaller one with bunks along the wall, the bunks decorated with wooden carvings that are beautifully crafted but difficult to photograph. There's more attractive decor around the hostel, statues and prints and paintings and dolls, giving it the air of a family home.
Security is a priority here: the door is opened by a code, and in the dorms there are very small lockers for passports, tickets and other compact valuables, as well as chains to secure larger bags and cases. As far as comfort goes, my capsule (and the rest, I assume) had just a single futon mattress on tatami, so while it was adequately comfortable, I wouldn't recommend it for light sleepers or sufferers from back pain.
Most memorable were the cheery, friendly staff, always happy to take time for a chat or to give information and recommendations; they also held an impromptu party one night (which I missed, unfortunately) with nihonshu and hand-made sushi. The kitchen is well kitted out, with a good big fridge, and also serves as the common room, though if you want to use the free Wi-Fi you'll need to stay upstairs, since for some reason that's available only in the dorms. There aren't many showers or toilets, but perfectly adequate for the small number of guests: the showers were clean, the water pressure good, and you could choose from toiletries provided by the hostel or left by previous guests.
It's literally a few seconds' walk from Nakano-Shimbashi station, on a spur of the Marunouchi subway line, so you'll usually need to change at Nakano-Sakaue: the journey to or from Shinjuku will take just seven or eight minutes. The neighbourhood is a peaceful residential one, but there are a decent number of stores, cafes, bars and restaurants nearby: you're well served if you like curry, with Japanese, Indian and south-east Asian options all close at hand. There are no landmark sights in the area, but if you have a free half hour it's worth walking the couple of minutes to see Hongo Hikawa shrine and Fukuju-In temple.
I couldn't find a way of booking directly on their website: I used a well-known website to make my reservation, and paid ¥2800 per night. So as well as being central and friendly, it's also great value!