Resources: http://www.japan-guide.com/e/e2164.html http://www.tourism.metro.tokyo.jp/english/
Tokyo is one of the best places to shop in Japan (but not the best in my opinion).

Shopping areas
*Area names are linked to maps

Shinjuku
Tokyo = Shinjuku
Everytime you hear about Tokyo, you'll think Shinjuku.

If you have a shopping list, it's probably here where you can fufil every single item.

Just on the top (and the same level) of Shinjuku Stn, there are 6 malls.
Odakyu, Keio, Lumine, Mylord, Lumine 2 and Est.
IMO, its enough to make you stay for at least 4hrs.
For Odakyu, there's a small budget cosmetics section on the 2nd floor where you can get your drugstore cosmetic fix.
Lumine, Lumine2, Mylord and Est have nice fashion items and equally appealing stores.

On the outside areas to the east, there is Alta, Isetan, Muji standalone store and Marui City.

Alta is similar to Lumine, catering to young females. Oh and there's a Mister Donut here.
The Muji is just next to Isetan and has about 4 or 5floors. Worth a peek.
The Isetan caters more to branded items, did not feel like there was much to see.
Marui City has Orbis in case you are interested.

To the south of the station, there's Takashimaya, Tokyu hands and Kinokuniya.
The Takashimaya here is pretty big and carries quite a few counter-brand cosmetics.
Tokyu hands is more for the creative arts and craft person.
Kinokuniya is pretty huge here, good for buying Japanese language textbooks :)

For your counter brand cosmetics fix, you can probably get everything at Odakyu or Takashimaya.

Kabuki-cho is actually an interesting place to walk plus there's quite abit of resonably priced eats in the alleys there. Yes it is a Yakuza area by the way, but don't let that discourage you. It's a very colourful neighbourhood.

Somewhere to the north of Odakyu there's an alley with lots of cheap yakitori joints called Shonben yokocho. Might want to visit if you are there in the evenings.

There is also a Bic camera and Yodobashi camera here.
Their respective websites actually publishes prices of items they carry.

Shibuya
I prefer this place way more than Shinjuku or Harajuku.

And I feel it's a must to have a drink at the Starbucks at Q-Front (a CD store like HMV) and watch as people cross the massively huge pedestrian crossing down below.

There are plenty of small independent shops here as well as trendy malls.
My favourites would be Parco 2 （There's Parco 1 and 3 too) and Loft.

Oh.. how I love Loft!
It has a massive drugstore skincare and cosmetic section, as well as all the stuff and gadgets you see in sprees.
And not forgetting the stationary section!
It's hard not to fall in love with Loft.

There is also the famous Shibuya 109 and 109-2. Somewhat like our Far east plaza?

There's also a standalone Uniqlo store somewhere near Parco 3.

Part 2 here