>>1
For models, Yellow Submarine and Kotobukiya are good (but many others sell models as well as display some really good examples of completed models). In general, the building that Yellow Submarine is in has tons of model shops. If you just walk around Akihabara you will find something. The Gundam Museum also has a shop that sells models.
Animate, Mandarake, Gamers, Toranoana, K-Books and many other stores have anime/manga stuff. Toranoana, Melon Books, K-Books and I think Mandarake have doujinshi as well. Yamagiwa Soft sells many anime/manga related games (although /t/ seems to have plenty of that already). If you really like Shonen Jump stuff, the Jump Store in Dome City is pretty cool (although they only sell Shonen Jump stuff).
Many anime/manga stores have their largest stores in Akihabara (and many are also split up into separate locations within Akihabara), but they also have stores in other places, like Ikebukuro (but many of the stores in Ikebukuro also specialize in yaoi, so unless you're into that kind of stuff, look before you enter).
Even convenience stores sell some anime/manga stuff. Sometimes they even have exclusive merchandise.