Japan is somewhat of a guitar paradise. Probably second only to America.
The japanese seem to take everything to the nth degree and guitar stores are no different. Typical guitar stores have floor stock that would total to an unimaginable amount of money. All on the floor for patrons to try and buy. Like I said: Guitar Paradise.
I didn't get to visit a lot of stores when I was over there. But here are some of the ones that I did visit:
Nico Nico Guitars
This one stands out from all the rest for me. Staff were friendly AND helpful. They were knowledgeable about CITES and provided useful advice.
Their guitar collection was outstanding. A real variety as well - there were old Gibson Les Pauls worth a fortune hanging on one wall, and on the other side there were way more affordable options. They are 100% second hand dealers...no new guitars. The guitars are well maintained and available to be tested out (I didn't ask to try any really expensive guitars though). And they wipe down the strings and guitar after you're done playing it...always a good sign.
Definitely one I'm going back to.
I tried a Sugi model with a HS configuration, and a Greco LP Junior type with a Bigsby. The Sugi was nice but it didn't really bond with me right away. The Greco was also nice with a cool finish however I wasn't really looking for a Bigsby equipped guitar.
HyperGuitars
Man, what a store.
Truly impressive collection of guitars...not just expensive but interesting as well. Spoke to the owner/shopkeeper who was very knowledgeable and helpful. He was also honest about what he perceived the risks to be (with CITES) with any shipping outside of Japan.
He admits to speaking little English but I think he's being modest, as I understood him well enough. Got to handle a couple of vintage telecasters which were on display. Another highlight of the trip for me.
TC Gakki
2 floors of good to great guitars from a range of price points. Their used guitar stock was considerable and interesting, however one that I tried was not set up properly IMO. Perhaps it is not in their policy to fix/set up their used stock below a certain price point - not going to fault them for this.
I tried out an Aria Pro II LS-600P. It was a Les Paul with P90s however with specs that are more common with Japanese guitars at the time (i.e. not "vintage specs"). I think it was a 3 piece maple neck into a mahogany "pancake" body and maple top. Ebony board. Beautiful guitar but as I said it wasn't set up properly and the strings were also dead.
I also tried out an Epiphone Wilshire from the 70s that had a homemade paint job :) They actually play really nicely...light guitars and not much to them.
The staff that helped me were good, you do have to approach them though. Once you do they are helpful and pleasant.
Oh and I also inspected an Ornetts there! I didn't play it through an amp though. My first encounter with an Ornetts and they are beautiful, although this one's paint job was not really my thing.
UNDERNEATH
Great place to check out some very cool guitars, effects and amps. Saw a vintage Binson Echorec there!
As far as guitars go, they have a very modest collection of used guitars, but some very interesting ones. Staff were friendly but I didn't ask to try any.
Ishibashi Shibuya
Probably the most well known music chain in Japan?
Their Shibuya store may not be their largest store but it is filled to the brim with guitars and basses. You can really spend a lot of time there...you basically can't look anywhere in the store without seeing a guitar!
Of course they had a lot of new guitars but I was more interested in the older ones. I saw a few interesting ones from Yamaha (the Flying Samurai) and a few Mosrite clones (well, not really clones...they did have their own spin).
There were also some cool Japanese only models from Fender. Took a pic of a model called the Haruna Telecaster - which seems to be a signature model of a female guitarist over there.