This was originally published on October 3, 2007. If you're reading this much later than that, stuff might well have changed. Tokyo doesn't stand still for long.
I lived in Tokyo for about two years, and here are a few of my favourite shops for buying games--second hand, new, and English language. It's notoriously difficult to find anywhere in Tokyo, so I've included a crap map.
Not surprisingly, the biggest concentration of video game shops is in Den Den Electric Town, otherwise known as Akihabara.
Akihabara area (JR Akihabara station)
This is like a video game graveyard--where old game consoles and games go when they're not quite ready to die. Over three floors, and filled with retro games including the Virtual Boy, SNES, all the way to the still very much alive and kicking PlayStation 2. The top floor is a small retro arcade, where you can sit and play favourite old games. Prices are reasonable.
Address: 3F Kitanayashi Bldg, 1-11-2 Soto-Kanda, Chiyoda-ku
Open: Mon-Fri 11am-8pm, Sat-Sun 10am-8pm
Web site: www.superpotato.com
Game and DVD Trader
Traders is a second hand DVD and video game chain, with several branches across Tokyo. There's also one on the Chuo-Dori. This is the biggest one I've ever been in, and has stacks of Nintendo DS and PlayStation games on the ground floor, along with some 'questionable' PC games.
Address : Sotokanda 1-4-9 Chiyoda-ku
Open: Mon, Tues, Wed 11am-8pm, Fri and Sat 10am-8.30pm, Thu, Sun, Holidays 10am-8pm
Web site: http://www.e-trader.jp/
Yodobashi Camera Akiba
Touted as the biggest electronics store in the world when it opened, I'm not sure how we can substantiate that, but it's certainly big. Very big. Games are on the seventh floor, along with toys, and it has probably the biggest selection in one place in all of Akihabara. However, titles are also a little more expensive than in some of the smaller outlets. Games sometimes get taken off the shelves faster than they can be restacked, so it's worth asking at the till if you can't find something. Taking the showa-dori exit from JR Akihabara station will bring you out right beside one of the entrances.
Address: 1-1 Kanda Hanaokacho, Chiyoda-ku
Open daily 9:30am-10pm
Web site: http://www.yodobashi.com/
Game Hollywood stocks import American games in all formats, which is handy if you live in Japan, love gaming, and don't speak Japanese. There's a wide selection of titles here, and new ones tend to show up fairly fast. You can also check on the handy Web site to see if what you want is in stock or not before you head out.
Address: 5th Floor, Uchida Building, Sotokanda 1-9-9 Chiyoda-ku
Open: Daily 11am to 8pm
Web site: http://www.gmh.jp/
Messe Sanoh Chaos
Moved to handily right next to Game Hollywood from its previous location up a dodgy staircase on the Chuo-Dori, Messe Sanoh is cheaper than Game Hollywood, and has a bigger PC foreign game section. It's worth trying here first, and if they don't have what you want, popping next door to Game Hollywood.
Address: 1st Floor Kankou Building, Sotokanda 1-9-11 Chiyoda-ku
Open: Mon, Tues, Wed 10.30am-8pm Thur, Sat 10am-8pm Fri 10am-8.30 Sun, Holidays 10am-7.30pm
Web site: http://www.messe.gr.jp/
Harajuku area (JR Harajuku)
This hilariously named chain of second hand book shops also stock a wide range of used video games and consoles in all the current formats. They also have sister stores called Hard Off that sell second hand hardware, if you hadn't finishedlaughing. This branch is the most centrally located, but it's worth venturing out into the suburbs for real bargains--for example the Ogikubo branch (just across the big crossing from the JR Ogikubo main exit) has a whole two bookshelves of games under 1,000 yen on all formats.
Address: 1-8-8 Jinguumae Shibuya-ku Tokyo (On the Meiji-Dori towards Shinjuku, just past the New Balance store.)
Open: daily 10am-9pm
Web site: http://bookoff.co.jp/index.html
Shibuya area (JR Shibuya)
This chain has apparently been around for a while, but I guess I never noticed it. Primarily a manga comic store, it's crammed full of manga comics, including rare and special editions, and also figures, posters, and cosplay costumes. They also have a game section, selling all the usual formats, plus a few retro bits and pieces.
Address: Shibuya Beam B2, 31-2 Udagawacho, Shibuya-Ku
Open: Daily from 12noon-8pm
Web site: http://www.mandarake.co.jp/english/shop/sby.html (English map on the Web site)
TheCrap Map of Akihabara
KEY Where 1-Super Potato 2-Game Hollywood 3-Messe Sanoh 4-Game and DVDTrader 5-Yodobashi Camera Akiba. More or less.