ROBOTROBOT - Nakano Broadway, Tokyo

Oh hell yeah.

One of the best retro toy collections this side of Tokyo, with a bunch of classic gaming stuff. From Parappa the Rapper to Sonic to MGS, with quite a few ultra rare pieces. 

Split over a few stores (similar to Mandrake) you'll need to do a bit of legwork to find this one, but absolutely worth taking some time out to hunt down.

http://www.robotrobot.com/hub/index.html
DD

Retrotailer - Droopy

A Narnia door to 80's, 90's awesomeness.

Simply put, the best retro you shop ever. The few pictures here don't do justice to the sheer quality or quantity of western toys from yesteryear.

Might Max, Ren and Stimpy, Boglins, Mario, Sonic, Pacman, Bucky O'hare, Ghostbusters, the list just goes on and on. Some major rarities include original '94 Mortal Kombat figures (all of them, including rare ones) and Street Fighter the Movie toys (all of them, including every VanDamm outfit ever produced). All items are retail or below retail price, however, quite a few are sold as sets, meaning quite a large investment both financially and in terms of space.

Can't stress how awesome this place and the staff are.
DD

〒166-0003 Tōkyō-to, Suginami-ku, Kōenjiminami, 2 Chome−26−5
http://goo.gl/maps/k2S4U