Japan has an amazing second-hand culture. The standards for selling used goods are very high there.
I mostly like to shop used merchandise and clothes, but also books, manga or anime figures. You can get some really good deals for stuff that looks as good as new.
When I went to Japan for the second time I even got an used famicon (Super Nintendo) with four games for only 30 bucks. We got it even cheaper because the color had already started fading a bit...
(But I would only recommend this if you speak/read Japanese, because they don't have English versions of the games.)
For my anime figure collection, I love to shop second-hand. I'd say that 80% of the contents of my showcase are used items – but they don't look like it.
Second-hand shops for clothes and fashion are not unusual and pretty much international, but there are stores in Japan that only sell used goods, especially merchandise, DVDs, video games or books. And those stores are no small individual places – they sometimes even have several floors, an unbelievable supply and even come in chains. So if you don't need the newest shit and can wait a few months to get it, take a look at the used goods stores in Japan. That way you also get them at reasonable prices. If you want to go “Otaku-Shopping” in Tokyo, I'd recommend visiting the districts Akihabara, Ikebukuro and Nakano – although you'll also find some great stores everywhere in Japan. Some famous chains to sell/buy used merchandise/manga/doujinshi are for example Surugaya, Mandarake, or K-Book.
When you go shopping for clothes, second-hand fashion doesn't always come at cheap prices, since a lot of those stores have special brands or vintage goods from the 80's/90's that are “stylish” again now. But if that's what you're after, you can buy some nice Levis overalls or a colorful Nike windbreaker for yourself. And if you're a real fashion queen/king, there are even a lot of luxury label second-hand shops, for brands like Louis Vuitton, Gucci or Comme des Garçon. And while you're trying on all this cool stuff, please keep the rules for fitting rooms in Japan in mind that I explained in the third issue.
A lot of those thrift stores are located in Harajuku – a fashion district that I'd highly recommend when you want to shop clothes. And while you're there, get a delicious crepe! They're sooo good!
Let me know in the comments what your favorite places for second-hand shopping are – and if you've ever tried a crepe in Harajuku!