If bookstores are your happy place you'll feel right at home at this hostel where the beds are fitted into bookshelves. The capsule-style bunks have privacy curtains and there are even ones with double beds (from ¥10,000). One downside: nonguests can pay to access the lounge during the day (from 1pm to 6pm), which can get crowded. Payment by credit card only.
While it's a drawback for guests, the open lounge space is great if you want to rest for a bit – before heading out to Shinjuku's bars and restaurants – but don't want to make the trek back to your own accommodation. It's ¥540 per hour or ¥1620 for the whole five hours; you can also rent a bunk (weekdays only and vacancy permitting) for ¥840 per hour for a nap.
Most of the books and magazines are in Japanese, but there are some good ones in English, including Japanese novels in translation.