In most places prices are shown clearly (including 5% tax), so you don't have to worry that you might get ripped-off. ;-)
I'd like to recommend to visit Omotesando - Harajuku.
Take Tokyo Metro (either Ginza line, Chiyoda line or Hanzomon line) and get off at Omotesando Station (A red mark on the map).
Walk along the street towards Harajuku - if you go out of the metro station, you'll be at a very big crossing with two gigantic stone lantarn and matured trees are lining on the both sides of the street. Go along this street.
On your right a new shopping mall called Omotesando Hills. You'll find many posh shops though they are very much pricy. There are many brand shops such as Dior, Louis Vuitton, Gucci, Fendi, Armani, just for example.
Go along the street and after 10-15 min walk, you'll find Oriental Bazar (the green arrow on the map, the one not very far from the red dot), with very distinctive shop with Japanese-like (not really) tiled roof and red columns. You'll find many traditional (and not so traditional) Japanese things, they carry a wide range of goods. Even just looking at the goods is fun, even for Japanese people!
Not very far from Oriental Bazar, there's a famous toy shop called Harajuku Kiddy Land (A on the map). There are many cute goods.
Again, walk along the street, then you'll reach a stone bridge over railways and Harajuku station of JR line. (The blue dot on the map.)
It is where you can see some young people in very interesting costumes on weekends. (If you have enough time, go across the bridge and then you can visit Meiji Shrine (the green part on the left of the map.) It is like a small forest, once you go into it, you cannot believe you're in the middle of the city!)
Turn right and go down the sloping road, and turn right again at the first corner (the yellow dot) and go into the narrow, crowded street. It is called Takeshita doori (Takeshita street) where there are hundreds of small shops selling inexpensive stuff. On your left you'll find Daiso, one of the famous 100Yen shop (to be exact, everything is 105 Yen because of 5% tax...)(Another green arrow near the yellow dot.)
They have 3 floors plus one basement, and you can buy almost anything from food to cosmetics, stationery, DIY tools, ornaments, party goods, gardening goods, etc. at JPY100/each. Only a few items are sold at JPY200, 300 or 500 but they are clearly marked.
Have a great time in Tokyo, and enjoy shopping!