Here is a list of some of the shops you should go to. The information provided here is correct to the best of my knoweledge. If anything has changed, please let me know.
The main shop for anime goodies is a chain called Animate. There are many stores basically everywhere. In the central Tokyo area, there is one in Ikebukuro and Shibuya. Further out there are some in Yokohama and Kichioji. All these stores sell the same stuff, but some may have larger stocks of some items than others. This store is usually the best place to buy the little items and other goodies. Try not to buy CDs, CD-roms, LDs, videos or books here as greater savings can be found elsewhere. They sell everything at full price.
This store operates a card scheme. Every time you spend 500 yen on items (1000 yen for AV stuff, books not in the scheme) you get a stamp on your card. A full card requires 20 stamps. Once your card is full, you can use it as 1000 yen towards your next payment there. Even after the card is used, keep it. When you have three used cards, you can exchange them for one of their own design phonecards.
Warning: Shopping in this store is highly dangerous. Make sure you have plenty of money especially on your first trip.
I will assume you will be arriving from the JR rail network stations. The underground stations are often close by.
Leave the train at Shibuya station using the south exit I think. It is at the opposite end from the Hachiko (the dog) exit. Just outside there are some toilets on the left and a bridge crossing the road nearby. Head across the bridges to a road which slopes upwards. There are also trees on that road I think. The shop is a little way up on the right side.
On trying to leave the (very big) station, follow the signs for the Sunshine Building. Outside, follow the road along a bit to a large junction/intersection. Cross the roads at the lights and proceed up the road in front. It is usually closed to traffic. Eventually you will pass the Sunshine building on your right. Keep going forwards and cross the road. Here you should be just outside a big Toyota (or was it Mitsubishi?) car showroom, as seen on Top Gear, the best motoring program on British TV. Go on a bit more to another road and follow the pavement right. Animate should be on your right.
Note: There is more than one floor to this shop. To get to the upper floors, you have to leave the ground floor first as the stairs are out in the front. I wish someone pointed that out to me as it took me about three months to find that out.
Leave the station at the East exit. Going forwards a bit should be a big post office on your right. Go past that, and follow the pavement to the right. There is a small shopping center. Go up one floor to Animate.
See also their web page here.
This store has mostly used manga, doujinshi, old or not generally avalible posters, cels, ufo dolls, CDs and various (older) items. It is like a second hand shop for anime. Some items I got in this store include, two Sailor Moon ufo dolls, some seiyuu posters that were originally given away with the 1st release of CDs, some posters used for advertising games and far too many cels (mostly Tenchi and Sailor Moon). This store is the place to go for old and currently unavailiable items.
I only know of two shops, both of which are in Ikebukuro. Follow the directions as for Animate. K-books is essentially next door to Animate. There is a sign on the pavement pointing in, you have to go up one floor for the shop. They have another shop nearby. If you face the road with this shop behind you, go left back to the junction. There is a small opening leading to a lift. Use that to go to the 8th floor. It is a small shop with doujinshi, posters and cels. I also found a UY vinly record there and bought it!
Also in Shibuya are some other stores, one called Mandarake selling various old stuff. It is a fair distance from the train station so you'll have to find someone to show you the way there. Find their advert in Newtype.
See also their web pages at http://www.mandarake.co.jp/.
There are many Totoro shops, although I only know of two, one in Harajuku, the other in Kamakura.
They both sell basically the same things, Totoro stuff.
A store in Akihabara which has many CDs, LDs, CD-ROMs.
See also
http://www.yamagiwa.co.jp/
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