You can bring your old clothes to H&M and say "Recycle (reeh-sai-kuru in Japanese) kudasai". They will take it and give you a 500 yen discount coupon, which can be used with purchases over 3000 yen.
Or just bring it to UNIQLO, they will send your clothes to developing countries.
If you want to sell unwanted stuffs, selling them online is better, like Craiglist.com. There are also some Yahoo Groups within Japan where you can buy and sell second hand items you do not need. Most of the members are foreigners as the main instructions use in the group is in English. Here are some groups where I am also one of its members:
TellandSellJapan -- where you can buy and sell unused items for prices of your choice
FreeStuffJapan -- where you can give for free any unused items you have to those who need them more