Here's a summary I did on another forum for auto related stuff:
Toyota Mega Web
見て乗って感じる クルマのテーマパーク MEGA WEB（メガウェブ）
This is a showcase of Toyota cars. They also have a History Garage that's in the building next to the Toyota showcase and it happens to be attached to a mall too! You can buy automobilia at the Euro Sports located inside the Toyota showroom or at the History Garage.
Super Autobacs
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Direct link to list of stores:
AUTOBACS.COM - X̂ē - X܌
It's like a big Lordco, except they have a couple of racks full of wheels and a lot of neat stuff. I went to the one at Tokyo Bay - Shinonome (3538'31.34"N 13948'12.19"E) it's huge! I followed these instructions someone had posted on Japan-Guide to get there (it's basically in the middle of nowhere):
Tokyo - Shin-Kiba (Keiyo Line)
In the station go through the gates and on your left there is another gate for a sep train line.
Shin Kiba - Shinonome. (NOT JR! Its like a Sep Line kinda like the Ginza - Costs 160yen IIRC) When you get out of the train, look towards the platform and you should see the store
Walk out Shinonome station with the 7/11 on your left (not a 7/11 anymore), Walk to the end of the street, turn right and cross 2 roads and you'll see the HUGE autobacs sign!!!!
Honda Collection Hall
Honda Worldwide | Honda Collection Hall
This is pretty much a full day trip. I think most would've heard about this place so not much to say. If you get there early enough go out for a ride in a stock car (like an NSX). One thing to note, it doesn't say this in English, but the buses only run on weekends.
Honda Welcome Plaza
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If you want to buy Honda Souvenirs without having to leave metro-Tokyo, visit this place in Aoyama. It's located just outside the subway station. You can also see Asimo here, he comes out to play a few times a day!
J's Racing
J'S RACING (DO NOT GIVE UP JAPAN)
J's Racing requires some travel from metro-Tokyo as it is located in Osaka, Japan. To get there take the bullet train Tokyo Station.
Spoon
SPOON OFFICIAL WEB
Spoon Sports can be found from the 1st station on the Oeido line. You'll have to walk a bit, also the address for spoon is the headquarters. Walk further down the road to Type One to purchase anything and to see the real "shop". A little out of the way but worth going to.
Mugen
| MUGEN official web site
No idea how to get here.
Audi Forum Tokyo
Audi Forum Tokyo > Audi Japan
Located in trendy Shibuya District in "the Iceberg" building. They seem to take the cosplay thing to an extreme in this district (at least when I was there a few years ago)!