Where to stay? (1) ---- Hotels

This is very important, how much are you willing to pay for good accommodation.
First, sort out your priorities. Do you want to pay as little as possible, be as comfortable as possible, or be as convenient as possible?
I would suggest make a list of criteria of things you must have in your place of accommodation. For example, if you want a private bathroom , bed or tatami/futon, shared or private room, location, amenities, nearby attractions, etc. Then, you start look for places at different locations and compare the prices, reviews, and location.
There are several types of accommodations to choose from.

1. Hotel
This is the most simple, and the most expensive choice. Hotel prices usually range from $12000 yen and up for 2 persons (approximately $120). Of course, the location and quality of the hotel is a determine factor of the price. The higher the star, the better location, the more expensive it will be. Most hotels have the basics: private bathroom, bed, bath robe or pajamas, slippers, hair brush, tooth brush and tooth paste, lotion, face cleanser, some would provide a razor, other toiletries, hair dryer, hot water machine , LAN, TV, mini fridge, etc. Pretty much what you would expect from a hotel. However, some hotels would charge money for bathrobes, so I suggest reading the hotel guides if you are unsure. Most hotels would have English guides for foreign guests. As for TV, some hotel would have a machine in the hall way that you can pay $1000 yen for a card to watch cable TV for a day. Most TV only have the basic channels. Most hotel rooms have adjustable AC and humidifier. Another benefit of staying at hotels is that they usually have direct transportation from and to the Narita and Haneda Airport.
When I book my flight to Japan from an agent, it came with a free 3 nights hotel stay. It was great, because the hotel had actual English speaking staff who can give me and my sister directions for places. Also, the location of the hotel is good, it was in Shinjuku, where there is a major train station for all the different lines. Also, there are various malls around the train station, making dining easier. My sister and I actually book our trip around where we are staying, to save a little on transportation cost.

The first hotel we stayed at was Shinjuku Washington hotel. It was pretty great, and the room was the biggest room we've stayed at for our entire trip. We had researched for more than half a year before booking a flight and the other hotels, and we've heard good things about this hotel. The staff was friendly, and some can speak English, making the process easier. There's a 24 hour convenient store at the ground floor of the hotel, so you don't have to go too far to get snacks. The location of the hotel was great! It is on the opposite side of Tokyo Metropolitan Government Building, so it is quite safe at night, and you can go check out the view of the observatory floor at night if you have nothing to do. It takes about 15 minutes of walk to get to the JR station, or you can take a bus, costs $100 yen (approxi. $1 dollar). The hotel also offers breakfast at $1300 yen ($13 dollar) per person. There' a few choices to breakfast when we stayed there, there's a Japanese style restaurant offering rice and fish breakfast set, a Cafe offering simple sandwich and coffee set, and the best is the breakfast buffet at the 25 floor. This is a popular choice, because the buffet have both western and Japaneses style cuisines for you to try. The view is good too, but you would need to go early to avoid lining up. I would recommend going as early as possible, because there's more seats you can choose, and you can enjoy your breakfast for as long as you like.

The second hotel we stayed at was at Akiake, a bit further away from the central Tokyo city. We stayed there because we wanted to attend a convention at Tokyo Bigsight, the Tokyo international exhibition center. The hotel is actually across from Tokyo Big sight. We stayed at the Tokyo Bay Akiake Washington Hotel, which is a chain of Washington hotel. We didn't pick this hotel because it was a chain of Washington Hotel, but because of the location. This hotel have direct transportation from and to the Narita and Haneda Airport with Limousine Buses, which I highly recommend. You should really consider this when you are leaving, because the luggage would be heavy, and you wouldn't want to drag them through the train stations. Trust me, because I did that when I switched hotels. It was a very unpleasant experience. Anyways, If you plan on going to Disney world or the sea world (?) , you should consider this hotel or other nearby hotels, because they also have direct buses to Disney land/world. It will save a lot of grief, because from what I've heard, Disney land is always packed, no matter which days you go. Another good thing about this hotel is that the building is very new, so the equipment and amenities are quite new. And they have the biggest bathroom, compare to the other places we've stayed at, and adjustable AC. As for transportation, the train station is very close to the hotel, and there are 2 different lines to choose from. Also, the hotel is just a bridge away from Odaiba, where there are many sights.
We've stayed there for a night, cost about $14000 yen, or $140 dollars for a semi-double room for 2. We didn't get a discount because it was around the Golden week, but if you went during off season, the price should be lower.

You should try booking through an agent first, because sometimes they would have discount. But you should also check prices online to see if it is a deal or not.
If you are traveling along, and you are female, some hotels have a female only floor for female customers. The hall ways are usually monitored, so safety is ensured. The room's amenities are usually more tailored to female customers, but there's usually only single, semi-double, or double rooms to choose from.