Where to find particular items in Japan for a more health conscious/sustainable life:
Apple cider vinegar - an organic one is available at Tokyu stores
Blueberries - are available in the frozen section year round of Ito Yokado, Seiyu, Yamada and Tokyu. Yamada is the cheapest. None of them are organic.
Unpackaged bread - I have had the best luck with Saint Germain and the Maruetsu bakery
Buckwheat flour - from Tengu Natural Foods http://store.alishan.jp/index.php.
Coffee - I love the Women's Hands organic fair trade coffee from Kaldi. YUM.
Clothing - questionable ethics for at least one of these stores aside, H&M and Muji sell a range of organic cotton basics such as underwear, leggings, socks, t-shirts for women, men and children.
Cranberries - organic ones from www.iherb.com - they deliver for a very reasonable price to Japan.
Jam - Tokyu store has some organic jam - there were four different flavours.
Linseed - www.iherb.com - they deliver for a very reasonable price to Japan.
Miso - organic available at Tokyu and Hanamasa
Natto - organic natto available at Tokyu stores
Prunes - organic ones available at Tokyu
Pukka teas - I have seen these awesome organic herbal teas at Rose Bakery in Ginza and Seijo Ishii stores. There is also a website www.pukkaherbs.jp. They are very pricey, so if you have mates in the UK - ask them to send you some! They are on iherb, but they will not ship to Japan.
Pumpkin seeds - www.iherb.com - they deliver organic ones for a very reasonable price to Japan (as of recently - they no longer ship these to Japan - will look for a new supplier when the need arises)
Soy milk - organic soy milk available at Tokyu and Ito Yokado supermarkets.
Scottish oats - www.iherb.com - they deliver for a very reasonable price to Japan.
Sesame seeds - organic ones available at Tokyu
Spelt flour - www.warabe.co.jp - Warabe Mura is a fab online site based in Gifu and sells organic spelt flour. I tried the Bob's Red Mill flour from Tengu Natural Foods and it sucked. You can also buy it at Grano (see health food stores).
Sultanas - organic ones available from Warabe Mura
Toilet paper - Coreless, recycled paper is available at Maruetsu in their own brand range.
Vegetables - To supplement your veggie boxes - Tokyu store has a decent range of organic veg.
Veggie boxes: http://www.on-the-slope.com/shop/index.php?main_page=page_7 - this is the English order form.
Veggie boxes: Warabe Mura has a veggie box service www.warabe.co.jp
Walnuts - bought in bulk (well, bulk sized for Japan) from Hanamasa bulk store. Bulk as in big bags, not as in fill your own container, sadly.
White flour - Tokyu store sells organic white flour in small 500g packets
Wholegrain oats - www.iherb.com - they deliver organic ones for a very reasonable price to Japan.
Wholemeal flour - from Ito Yokado supermarket - found in the home baking section in some stores. Currently (March 2014), my local store is not carrying it. Tokyu supermarket also has small packets of wholemeal flour. It can be ordered from Warabe Mura and also from Tengu Natural Foods.
Health food stores:
Grano - Koshigaya Laketown, Mori Building, Ground Floor, Garden Walk