The last two times I went to Tokyo I stayed in the Hotel Villa Fontaine in Shiodome. Their rates are pretty good (I paid around US$90-100 a night) and the rooms are a decent size.
Shiodome has easy access to Akihabara and Ginza, as well as Odaiba. The closest station of the Yamanote Line is about a 5-minute walk from Shidome Shio-site, where the Villa Fontaine is located.
There are a few other locations for the Hotel Villa Fontaine besides Shiodome.
http://www.villa-fontaine.co.jp/eng/
As danth and wlfx mentioned, the Broadway Building in Nakano is a pretty good place for anme, manga, and video game merchandise. I have to admit that I am a bit biased toward the Broadway Building because a friend of mine and her husband happen to own one of the stores there.