Just a couple of highlights from this trip. I visit Kichijoji almost every time I go to Tokyo.
Avril - アヴリル吉祥寺店
Avril is the same company as Habu Textiles in NYC. If you are a knitter or weaver, this store is a must. All the yarns are on cones and they'll sell you as much as you need, so have a pattern in mind and the yarn requirements with you when you go. Labels are all in Japanese, but if you know Katakana you can generally sound them out. The yarn you receive will also be coned and the labels in Japanese, so you may wish to take your own notes of your purchases.
John Henry's Study - ジヨン、ヘンリーの書斎
This is a small cafe on an upper floor in the heart of the Kichijoji shopping district. You have to climb some steep, narrow steps to get there, but it's worth it. The decor is unusual and they serve the most flavorful mushroom cream sauce I've ever had.