Acommodations
Hotels (regular)
Standard hotels to luxury hotels, there are a wide variety of options available for your accommodations including some American hotel chains such as Hilton and Best Western in some cities. When searching for a standard hotel, be sure to explore other areas than just Tokyo such as Asakusa, Akihabara, Yokohama, etc.
Hotels (business)
Business hotel chains such as APA hotels offer lower hotel rates than regular hotels (~$80-$100 a night), but you do get what you pay for. Most business hotels are quite basic and can be noticeably smaller than the regular hotels. However, if you're on a tight budget, business hotels can be a great bang for your buck if you don't mind skipping a few amenities. Just be sure to get a non-smoking room as smoking rooms can be quite repulsive even if you are a smoker.
Hotels (capsule)
Capsule hotels are pretty self-explanatory. It's basically a long, narrow capsule bed that you can stay at overnight or even for your whole trip if you're on a budget. They can be quite inexpensive to stay at compared to other hotels. Bathrooms are often shared on each floor and genders are separated on different floors. It may be worth a stay for one night for the experience, but may not be for you if you are claustrophobic. The capsule walls are often thin and so noise may become an issue as well as inadequate ventilation in the capsules. Still worth researching if you want a cheap overnight stay if you want to extend your day trip in the prefecture you are visiting.
Hotels (love)
Love hotels are well...for short stays....and....you know. They can be rented out for a few hours to overnight stays. Most rooms are equipped for....love and include certain amenities. It may be worth a stay if you want to try something different and strange. Some rooms have a certain theme to them and you can find lots of unusual rooms with unique decor.
Ryokans
Ryokans are traditional Japanese inns that are akin to a 'bed and breakfast' type of accommodation. The rooms often feature tatami matted rooms with Japanese furniture and basic features. Some ryokans even have a private onsen bath in the room. They also have public onsens as well, which are nude baths and often segregated by gender. Popular areas for ryokans include Kyoto, Osaka, Aomori, and Hakodate to name a few. Be sure to look around for some deals and be sure to book way in advance as they can get booked up very quickly!
Machiya (traditional townhouse)
Machiya are traditional Japanese wooden townhouses that were used as both a residence and a place of business in the past. Popular areas to stay at a machiya include Kyoto, Kanazawa, Takayama, Kurashiki and more. There are even some with open air baths and other luxurious amenities.
Air bnb
Air bnb's are widely available in Japan despite the government regluations requiring Air bnb hosts to register their property and obtain a license number. While I personally have not utilized Air bnb in Japan, it can be another great budget option if you're looking to save money or don't mind having a private room in a share house. Be sure to do your research and thoroughly comb through the reviews to ensure your stay will be hassle free.