Once again it's time to copy my Tokyo information that Eric once posted here, hope this helps:
in general a good reference for tokyo shopping tourism -- and nyc and sydney, too -- is superfuture:
it's not specifically about sneakers but there are some really invaluable maps, esp. given 1. how complex it is to decode addresses in tokyo and 2. how difficult it may be to get help if you don't speak japanese (you'd be surprised).
a general caveat: if there appears to be a line outside of a shop... most likely that means there is a queue to enter! if you're going on a weekend to harajuku or perhaps a bathing ape in aoyama, pay attention...
if this is your first time to tokyo and you don't have anyone -- read: someone who can communicate in japanese -- to guide you around, your best bet is to stick with harajuku, shibuya, shinjuku, and perhaps aoyama. the first thing you should realize is that all of the hot kicks -- at least in japanese eyes -- are gone... long gone. reservations are taken at many places, and for example, some stores had already accounted for their entire stock of sheeds a while ago, and those don't come out until april. of course, whether all of these people actually buy the shoes upon release is another thing... but if the shoes are popular, the release is limited, and the quality is good... don't expect to pay retail unless you're an extreme size (big or small). an example would be the wheat/wheat-dark mocha air force 1s from around xmas... retail was 9,000 but fat chance finding those for less than 19,800.
on the other hand, if quality isn't particularly good -- and many of the newer nike releases have been quite poor -- then you'll have a chance to buy at retail. when i was there in late jan i was able to find a lot of pairs of white/black air force 1 lows, white/black patent air force 1 mids, white/orange-black dunk low pro b's, white/black ace 83s, etc., at retail, which i found to be quite surprising... but then each of these shoes tended to have widespread but small quality issues.
a good place to start is harajuku. get to either the jr harajuku station or the eidan meiji-jingumae station and walk down omote-sando. take the first left after meiji-dori (the main street with sephora, laforet, etc.)... on this street you'll find quite a few sneaker shops, including chapter, atmos, jump, zoom, etc., plus places like recon and neighborhood (and apparently a bathing ape shop but i've never been able to find it). chapter tends to have a wide selection, including things like the independence day air force 1 mids, l.a. air force 1 lows, etc... but expect to pay top dollar, if not more. the only thing helping you here is the exchange rate, as the yen is doing quite poorly against the u.s. dollar right now. also in the general area are headporter, stssy, and numerous like shops.
if you had taken the third left after meiji-dori, you'd come across a shop called "ad21" (it's above the real mad hectic shop)... it's basically a super sleek nike shop that in late jan was displaying the movement presto faze and the 01 line of limited clothing... not a lot of selection but i guess that's not the point.
as an aside, apparently the really fashionable thing in japan right now is making your shop so extremely difficult to find from the street that, well, people often do not find it. perhaps someone fell asleep during business school or perhaps they're doing so insanely well that they don't need business... i don't know.
so you've seen the enemy and waited in line... now you can try your luck in shibuya. walk towards the tower records and you'll find a little stretch with another, much smaller chapter shop, shoe bar, abc mart, etc. abc mart is huge but in reality tends not to have the really hot stuff in stock, while shoe bar seems to favor other brands than nike. across the street from shoe bar and abc mart is oi one, which on the 3rd and 4th floors has a large nike shop. when i was there you'd find all the reject, would be hot shoes on sale, like the suede dunk low pro bs, the new footscapes, and the not so nice colors of air zoom seismics.
in shinjuku there's more department store shopping -- don't laugh, i once saw the brazil dunk lows on sale at takashimaya -- and there's a little stretch on the way to kabukicho -- where you can most likely indulge in some of the stuff mentioned in a previous post -- that has 3-4 sneaker shops. selection is kind of hit or miss but you might find some nice buys from a few years ago or even some hot shoes if you search hard enough. if you make it to the shinjuku prince/pepe building, there's an athlete's foot in there, too.
there's also a large nike shop in kichijoji...
so what you're eventually going to realize is that besides chapter, you're going to see the same 50-100 pairs of shoes over and over and over again... and that none of the hot ones are available. at this point you might realize that it would be far better to try a suburb or even osaka, where arguably the selection might be just as screwed but at least the prices seem to be slightly better than tokyo.
after many ultimately disappointing trips to tokyo, i find myself going to a few shops near the gakudai-geigaku train station (a suburb) and mail ordering (and shipping to my hotel) from places outside of tokyo before i arrive.
if you're into electronics, don't forget akihabara... though you'll notice that the same thing that can be said about sneaker shops applies to the electronics shops there.
when all is said and done... take that money you would have spent on whatever pair of hot kicks you wanted and go get yourself some really expensive sushi. there's this absolutely incredible place called kozasa-sushi in ginza... take the b5 exit at the eidan ginza station and walk 3+ blocks down namiki dori (past the louis vuitton and on the same block as bally) turn left into the alley right before the "ginza nobu" shop and the lambo/audi dealership display and go into the first door on the right... it will have a double c with leafy branch logo. if you come across an elevated highway, you've walked too far.
try to go right when they're starting dinner service at 6pm as it's a tiny shop, reputed to be on the best places in tokyo, and it's going to be tough any later without reservations... but take your 19,800 that you would have spent on the wheat/wheat-dark mocha air force 1s and completely redefine what the word sushi means to you.
(try not to go on wednesday or sundays as the tsukiji fish market is supposed to be closed on those days, so the fish, depending on what you eat, might not be as fresh.)
hope this helps.
Just to add some details to Eric's email
Have to give UP's to Ceddie and Eric. That email has excellent info =)
I was in Tokyo in the past Oct. So just a few more pointers:
1) As mentioned above: "harajuku. get to either the jr harajuku station or the eidan meiji-jingumae station and walk down omote-sando. take the first left after meiji-dori" (quote) ..... REMEMBER he said the first left AFTER the meiji-dori.... not right at meiji-dori.... I think there is a GAP there.... go PASS the GAP (or whatever store at the intersection), stay LEFT and try to make a sharp left turn into a really, really SMALL street (I think it is right before a fast-food place... wendy's???) I missed that street 3 times before finding it correctly. You will see (within 1 min) after enterning the street a RECON store on your right (people lining up to get in.... ridiculous) and ATOMS store on your left (dude, HAVE to check it out... price is real high, but they sometimes got exclusive cross-products with other brands...like Gravis and Nike). Stussy, Head Porter, numerous sneaker stores are within that area.... go print out the map from superfuture.com and it will HELP =) But I mean, most stores got NO sign.... a Japanese trendy thing or something.... made me got lost so many times.... and hey, Bristol FCRB (Nike x some Jap designer super limited clothing line) is close by, but I don't know how to describe to you..... maybe a simpler way is to look it up from superfuture.com... basically it is just go back to meiji-dori (the main street you passed by before), walk in the direction AWAY from where you were coming, until almost the end of it (I think there is a diesel store), turn right with the road, and walk a little... the store is on your right, and again, with NO sign.... the significant part is that the store has all glass "automatic" door...
2) Shibuya. Nike shop. Must see, IMO. Got lots of Japanese exclusive Nike clothing (I like the material.... really hi-tech stuffs, they claimed =) across the street of the Nike shop plaza, you will see a shoe store.... I think... that one has some interesting stuffs too... but I mean, as mentioned before, almost all places carry the same set of old school kicks (popular in JP right now...), and the prices are ridiculous....
3) Last pointer... I have to say I agree with what was said before. Save the money for something else. Ha, I have to say that I maybe bias because I wear size 12 (which is close to impossible to find in Tokyo... unless in real big stores...). I mean, if you love COJP stuffs, you probably can get them here just as much as over there.... the thing is maybe you will find bigger selection there... good luck =)
P.S. - Electronic gadget shopping is a bit better though, I have to say... at least you will see models that you will NEVER see outside of Japan... so that justifies more on WHY you are willing to pay the price... and plus, VIDEO GAMES shopping is excellent too. Lots of old games.... Nintendo 8-bit.... hahahaha....
I meant ATMOS store. (not ATOMS). They had ATMOS x Gravis shoes, and ATMOS x Nike shoes before. I mean, at least "worth" checking out, even when you don't intend to buy anything...
Another thing, if you want to get some Jap clothing, should check out UNIQLO stores (chain store, all over the place, I think). Clothes are quite reasonably priced, and quality is quite good.
(Don'tread this sentence.)