I just got back from Japan! I did a lot of research before I went, but I was still totally unprepared in some cases for directions, what to expect, etc. Therefore, I'm putting together a guide to include the kind of things I would have found super useful to know before I went so other people will have an easier time!
Akihabara is a must-go. It's otaku Times Square. You will probably OD on anime goods in the very first store you go into, and there are HUNDREDS of them. It's also very easy to get to, being a major stop & transfer point on both the Tokyo Metro and JR Rail (below ground and above ground train networks). There's a good chance you'll have to do a line change at some point, so you can save fare by walking around since you'll have to swipe out/on to different train lines anyway.
However, it's also the sketchiest part of Tokyo that I went to. It definitely catered to dudes, with probably >90% male shoppers, and most of the female shoppers being foreign tourists. There are stores dedicated entirely to anime/manga porn (see welcome sign above), but even the non-porn stores have a lot of porn. It was kind of like going to a MLP convention expecting to see lots of cute pony stuff but when you get there you realize it's actually a Brony convention and there were a couple of cute things but mostly it was really weird porn and you start to question your life decisions and humanity in general.
The sketchy increases the later you go, with maid cafes sending out girls in fairly revealing maid outfits out to attract customers to their shops around sunset, and the crowd becoming generally rowdier/drunker as the night goes on. I'd suggest timing your visit with that in mind depending on your preference!
Now let's get to the doll stuff!
Stop #1: Volks Dollpoint Akihabara
Address: (English) Japan, Tokyo, Chiyoda, Sotokanda, 1 Chome−15 (Japanese) 東京都千代田区外神田１丁目１５
Website: volks.co.jp
Hours: M-F 11AM-8PM, Sat-Sun, 10AM-8PM
How to get there: Go to Akihabara station via Tokyo Metro or JR lines. The closest station exit is the "Electric Town" exit. Radio Kaikan is right next to the station, which also houses a mini mall of eateries.
How to find it: Volks Dollpoint is on the 8th Floor of the Radio Kaikan building (one floor above the Azone/Obitsu store!) You might be confused by the Volks Akihabara Hobby Tengoku store on the corner, a couple of doors down with red awning. The two are completely unconnected and have different hours. Look for the bright yellow signage (Akihabara Radiokaikan is written above the entrance in English). 
Every floor of the Radio Kaikan building is full of small anime, doll, and hobby shops. The whole building is worth a check out, since a lot of the stores have some doll bits (some marked down!) and rement (miniatures) even if you're not into anime, which is like 90% of everything else in this building.
Dollpoint is where you can go to maybe get a OOAK D'Coord display doll or have a Dream Choice doll made for you in addition to buying standard release dolls, clothes, bodies, parts, eyes, wigs, etc of both vinyl Dollfie Dreams and resin Dollfies. In addition to D'Coord and Dream Choice, there are some items that are only available here. So basically if you like dolls, you want to come here for one reason or another!
What you need to know:
- Volks has signs everywhere telling you what is OK to take pictures of (this is super handy since most Japanese stores have policies on what you can take pictures of). Generally displays and display dolls were OK for pictures, but items for sale like clothes, were not. There were stands of model heads you can choose from if you do the Dream Choice that I did not take pictures of because they weren't marked OK to take pictures of, for example.
- D'Coord dolls are one-off display dolls that are put out once a month at random times at both Dollpoint Akihabara and the Volks Yokohama store. If you really want a D'Coord exclusive head sculpt, consider visiting or asking at Yokohama. There are also seasonal exclusive skintones only available this way.
- Dream Choice is only available at Dollpoint Akihabara. You get to look through a book of bodies, heads, faceups, wigs, eyes, etc, and pick out the combination you want for your perfect doll. You may need to make an appointment (you can call ahead if you're in Japan, but you can also sign up in the store), if you go earlier in the day on a weekday you'll probably be able to just sign up when you get there for a slot while you're there. Like D'Coord, there are also seasonal exclusive skintones.
- They do tax free if your order is over 5,000 yen (about $50 USD), so make sure to bring your passport. It's good to have your passport ready with your wallet, since if you get a non-english speaking person at the cash register, they don't have to be nervous about asking you if you're a foreigner and you don't have to be nervous about asking them about tax-free stuff.
Way, way more pictures in my Volks Dollpoint Album
My notes: I'm a jaded doll collector and I was completely overwhelmed the first time I walked in here! So many excellent dollies! They're also fantastic at customer service, even for Japan which is fantastic at customer service in general. I hadn't decided whether I wanted a D'Coord or a Dream Choice doll when I went there. There are tags on some of the dolls with prices, but I couldn't tell if they were actual D'coords because those that were left (new models are put out randomly once a month) were all together on the same table. I asked one of the clerks about the doll I liked most (a D'Coord DDH-11), and he said that one wasn't for sale. I asked if he knew if there was a DDH-11 at the Yokohama store, because I was willing to check there in case they had one (D'Coords are also available at the Yokohama doll store, a bit over an hour's train ride from the Akihabara store) and if not, I'd set up an appointment to make a Dream Choice doll. He said he'd check at to Yokohama doll store for me, and to check back at 2PM (it was a little before 1). So I did, and holy crap he had the doll for me! Either they had someone bring the doll from Yokohama or they pulled out a D'Coord they had in the back for me. Utterly above and beyond, I was super, super happy.
Verdict: Go there!
Stop #2: Azone & other 7th floor shops
You may hit up the 7th floor depending on whether you work your way from the top down or the bottom up of the Radio Kaikan building. It's all escalators both ways.
Address: 101-0021 Tokyo, Chiyoda, 外神田1丁目15-16 ラジオ会館７階
Website: www.azone-int.co.jp/
Hours: M-Su 11AM-8PM
How to get there: Exactly the same place as the Volks store, just 1 floor down!
(More pics from the Azone store Here)
What you need to know:- This place is pretty well stocked mostly for customizing purposes (bodies, heads, wigs, clothes, etc.) For bargains, you can buy some nude dolls...which are marked down but not exactly bargains
- They carry lots of different dolls (like Pullip and the FR Nippon lines) but not a very big selection.
- I found the displays to be the best part, as the displays had lots of HTF and sold out dolls...you just can't buy them.
- Honestly I think I've been spoiled by their excellent network of US retailers, and US-shipping Japan-based stores.
- The store next to Azone had a huge Pullip and Blythe display case out in front of their store, and pretty good selections inside! Definitely pop in there if you're already going to Azone.
Address: 101-0021 Tokyo, Chiyoda, 外神田1丁目15-16 ラジオ会館７階Website: www.azone-int.co.jp/
Hours: M-Su Noon-8PM
How to get there: Go out of the Radio Kaikan store and take a left. There's a big intersection at the Volks store with crosswalks. Cross up and over to the other side of the street and go one block. Cross that street and turn left. Go down the first alley on the right you go to, and the Mandarake store should be directly across the street at the end of the alley. Look for the big red vertical banner signs on a narrow dark blue corner building.
Given the massive amount of EVERYTHING Mandarake has on their website, I expected it would be bigger. Hmm... nope! The doll floor was about 25' long by 15' wide. It was absolutely packed with doll stuff though.
What you need to know:
- Having gone straight from the Volks store to Mandarake, I can tell you that for things that both places had in stock, Volks was generally the same or cheaper for new things. Used things were generally more expensive than you'd be able to find on Facebook doll sales groups/doll forums/auction websites, but for the HTF, this is worth checking out. You MIGHT find something rare you can't find anywhere else, and in that case, it's probably worth it.
- Half the floor is resin & vinyl BJDs, the other half is for like, Blythe, Pullip, and other smaller/fashion dolls
- There are bins on the floor of clothes and other cheaper priced bits sorted by type/size. This is where you'll most likely find bargains--cheap wigs, shoes, etc. Nothing special, but you can't beat a decent quality pair of shoes or wig for $15.
- Treat each floor like a separate store. Pay for what you get on that floor, then go down to the first floor and show your receipt(s) to get a tax refund in cash.
- Remember what I said about sketchy? This absolutely applies. You may need to wash any 'used' doll clothes you get, for reasons.
- Also, the 4th floor is porn doujinshi.
- So is some of the 5th, but this is 'girl doujinshi' so it's less graphic/fetish but also a lot of yaoi.
Verdict: While a bit of a let down, if you're in Akihabara, go there. You might get lucky!
These aren't the only places you'll find dolls, but they are the major ones. There's a store that specializes in resin called DOLK across the river from the train stations, but I did not go there. You'll also find the odd doll in anime stores because there are so many licensed anime tie ins among Pullip, Volks, and Azone/Obitsu dolls. If you have time, totally wander around and go treasure hunting, especially if you go earlier in the day when it's not very crowded.
Akihabara is also the place to go for re-ment. You can buy blind boxes at good prices (about 100 yen/box cheaper than at Japanese toy stores), discounted full-box sets, and go into stores that specialize in selling opened blind boxes and capsule toys--for 2-3x the price of a blind box (which can still be worth it if you're looking for one set in a box). I did NOT see any old or rare re-ment though, and I saw more re-ment than dolls!