Here are some Tokyo shops & cafes of my recommendation:
/// NAKAMEGURO - DAIKANYAMA ///
*Daikanyama and Nakameguro are in walking distance, as well as Nakameguro - Yutenji - Gakugeidaigaku.
La vie a la campagne - beautiful French cafe
Meguro Gawa Canal - BEAT spot for sakura
COW BOOKS (pics here #1 & #2)
1LDK - selected mens clothing, their new shop for homeware & zakka "1LDK apartments" opened right across from this store
TASTE & SENSE - lovely cafe run by 1LDK, great lunch and great coffee.
TSUTAYA SHOTEN - mega book store that is more than just a book store
COCCA - v. charming fabric shop
/// GAKUGEIDAIGAKU - YUTENJI ///
Gallery & Shop "DO" at Claska
monogram - cute little shop for photography print & zakka
digawel - mens and womens clothing (yutenji)
keats cafe - vegetarian cafe set up in an old japanese house (yutenji)
cafe margo - lovely little cafe - excellent food and atmosphere
OTSU Furniture - Japanese vintage furniture
*My very favourite shop of all time "baden baden" has closed at the end of 2012 (sad!)
/// ROPPONGI - AZABUJUBAN ///
UGUiSU the little shoppe- my shop that opens on Friday, Saturday & Sunday afternoons!
21_21 Design Sight - an innovative and fun design museum
MORI ART MUSEUM - on the 53rd floor of Roppongi Hills Mori Tower
THE NATIONAL ARTS CENTER - great architecture and excellent design shop downstairs
LIVING MOTIF at AXIS - amazing design shop, bookstore downstairs has a wonderful selection of art & photography books
TSUTAYA TOKYO ROPPONGI - great selection of art books & magazines
TOUCH - really beautiful high quality towels and linen
*More recommendation from this area will be coming soon!!
/// AOYAMA - OMOTESANDO ///
doinel - lovely zakka shop that also has a great selection of organic wine
mina perhonen piece - one of other shops of mina perhonen in tokyo
Pan to Espresso to (Italian coffee and bread)
ARTS & SCIENCE - Beautiful beautiful shop!
SPIRAL MARKET - great design shop
gallerie doux dimanche - lovely lovely shop/gallery that hosts many interesting exhibitions by young and independent artists from all over the world
/// JIYUGAOKA ///
cafe ikanika - beautiful and relaxing atmosphere, my all time favorite!
cafe ohanaya - great Italian style food using fresh vegetables from Kamakura, also serves good coffee and organic wine
JIYUGAOKA BAKE SHOP - top floor of IDEE
Cafe 6-chome - cafe & vintage Japanese furniture
KOSOAN - Old Japanese cafe
gallerie doux dimanche - dear little shop full of young artists goods from all over the world
SHINA-JINA - lovely little modern bonsai shop
Yakumo Saryo / Baishinka Tea House - really really beautiful Japanese tea house, 20min+ walk from Jiyugaoka or Toritsudaigaku Station.
/// FUTAKOTAMAGAWA ///
*Futakotamagawa is about 5 mins from Jiyugaoka on a local train Oimachi line
KOHORO - Japanese tableware, homeware, zakka
BOX & NEEDLE - a shop full of beautifully crafted boxes from Kyoto - a real gem!
/// GINZA ///
Gekkoso - wonderful little basement shop full of art supplies
Dover Street Market Ginza & Rose Bakery (cafe)
Beer Lupulin - Japanese craft beer (microbrewery)
Rose Bakery - Marunouchi (near Tokyo Station)
/// NIHONBASHI ///
HAIBARA - beautiful washi store
MORIOKA SHOTEN - amazing book store that sell vintage art books
TAMAI - anago restaurant
MORINOEN - my favourite hoji-cha tea store
Details are in this post - QUICK GUIDE TO NIHONBASHI
/// OTHER AREAS OUT OF TOKYO ///
MUSEUMS & GALLERY