https://www.odigo.jp/articles/7001-experience-japan-while-you-sleep-the-ultimate-list-of-unique-and-unique-while-on-the-cheap-accomodations-part-i
Unique on the cheap
Love Hotel
The love hotel is a true gem for those on a budget. Love hotels were built in 1968 as an escape for couple to spend ‘quality time’ together. The main idea of paying by the hour originates from this concept.
Capsule Hotel
Capsule Hotels is a hotel developed in Japan and features a large number of small ‘rooms’ intented to provide cheap overnight accommodation for quests who do not require the standard services from conventional hotels. The main target of these hotels used to be businessmen who couldn’t make their way home on time and spend the night in one of the capsule hotels. However, capsule hotels gained popularity and are used by a great variety of guests (without claustrophobia. Please keep this is mind!).


Manga Cafe
Manga is a type of Japanese comic drawing style. Manga books, can therefore best be compared to comic books. However, Manga books can have a wide range of genres: From Comedy to Drama and from Romance to Fantasy and adventure.

Overnight Trains (or Bus)
Overnight are a great budget option to spend the night. You pay a fee to ride the train/bus (might even be free when using the JR rail pass) and you skip the time you need for travelling during the day by making the trip at night.
Due to the popularity of low cost budget airlines and overnight buses the overnight trains have decreased and two remain running to this day.
The Sunrise Izumo and Sunrise Seto remain travelling from Tokyo to respectively Izumo and Takamatsu.
You are assigned a 'seat' which is in reality a form of a bunk bed where you are also given a blanket and have your own reading light to keep yourself comfortable during the ride. On the train you can use the toilets and shower utilities making this a great experience on a budget and which will also save you a great amount of time.