Nakano Broadway is a good place to go for shopping of anime and other related goods.
Nakano Broadway is a mall at the end of the red line (I believe it's red? It was when I went in 2009) subway/metro.
It's different from the other malls I visited in Tokyo, but it wasn't a bad different. It was quieter, and had a LOT more collectors items and products. I found a shop that sells used books, magazines and even concert goods from popular artists in Japan, this is why I was going there. But I also saw a HUGE manga and comic book store. And with every corners I turned, there was a store selling anime figurines! There were even cosplay costume shops!
You can read more about it here:
Tokyo Qool - Nakano Broadway
I had a hard time getting there, I got up 2 stops too early and ended up taking a cab there because I was completely lost.
You have to get off at the VERY LAST stop, because there are 3 stops on the subway/metro map that say Nakano. The last stop is right next to the mall, so you can't really miss it.