I've been meaning to post this for a while, but here are the maps I used to highlight points of interest and shopping locations during our trip to Japan last year (you can read my journal on it here). I also left in some landmarks we visited if you're looking for things to occupy your time. Please be aware that these maps are by no means exhaustive, but it should be a decent place to start if you've never been to the country. I hope it proves useful to you.
You can click on the "->" icon indicator on the top left of the map to expand the legend and all the stores, or the [ ] indicator at the top right to bring up each city in a new, larger tab. Some special notes below:
If there's any city in the world that's too dense to map thoroughly without visiting a hundred times, it's Tokyo. I didn't get to half of the shops I marked out, if that. Shibuya is absolutely insane, but you'll also find great stuff in Shimokitazawa (a younger, hip area 15 minutes west by train especially good for vintage and secondhand shops), Ginza for luxury stores, and Shinjuku.
Wanariya, the small shop we visited to try our hand at indigo dyeing, lies to the northeast in Taito (marked #12). And if you've never seen the Anthony Bourdain special on Tokyo, Robot Restaurant in Shinjuku is an experience like no other. I'm not sure how else to put it.
Strolling through the streets of Kyoto feels like walking into the most beautiful time capsule. Between the temples, bamboo forest, and the older parts of the city, you could easily spend weeks here alone and never run out of things to do. If you head to Kiyomizu-dera for the day, make sure to stop at some of the ceramics shops on the walk up - something Kyoto is world-famous for.
You'll also find a surprising amount of great menswear. Real McCoys, Kapital, and a handful of great secondhand shops are all clustered in one of the main shopping areas. If you're walking up the street where Real McCoys and Urban Research are, there's a nice little vintage woodblock print shop up on the left you owe yourself to check out. Finally, Aritsugu Knives in the Kyoto food market is a top tier level knife shop if you're in the market. Be warned they only take cash. Shigeharu is another (perhaps even more so but a very small shop), though they were out of knives on the day we made the trek out.
Start on the Dotonbori and walk north on Shinsaibashisuji shopping street. In the evenings, the street swells into a two-way whitewater river of people, but it's much more manageable during the daytime if you're a curmudgeon like myself. To the north you'll find Strasburgo, favorite store of Akihiko Nishi. Cross the highway to the west into Minamihorie and you'll find a younger part of the city and some nice boutiques. The Jam store, an especially good American/Western heritage vintage shop, is absolutely massive.
If you've been to Japan or are visiting soon, please email me or let me know in the comments below if you've found any other gems that I missed on your travels.