One definite place to start is by reading my original post on this, how to find organic/natural personal care products, and if you haven't, definitely start there for some great ideas.
However, in this post, I just want to highlight a few organic cosmetic websites (many are stores you can order from as well), that feature various products and brands (so no one-brand sites here), and many of the products are actually Japanese. I've found some great items via some of these sites, and even though the language is all Japanese, you can definitely use a tool like Google translate or similar to help you out.
*And no, I'm not being paid by any of these places to list them here (I wish!) - I just thought they were interesting and wanted to share.
This site is probably my favorite of the list I'm including here, mostly because of its clean and simple layout. Granted, the selection isn't huge, but there are some great finds here. In fact, I just ordered a nice aloe moisturizer from them (free of additives and bad chemicals), and they even sent me a free washcloth/hand towel as a thank you gift. (That's the kind of service that'll keep me coming back!)
The Organic Beauty Store
Similar to Organic Cosme, with perhaps just a slightly larger selection. Some brands are the same as what Organic Cosme has, and some are different, so it provides variety. (You can also see my little Rikaikun box popping up in the image below - so now you know, if you didn't already, what "organic" is in Japanese [also, 有機] and that "cosme" is short for cosmetics. I've also already listed a bunch of words to know in how to find natural/organic personal care products.)
Lohas Cosme e-shop
Again, varying brands from the two sites I've listed above plus some more. Decent selection.
Not an organic store, but they do have an organic section with different products and brands. I've included the link directly to that section above.
Most of the brands here are imported, but they aren't all the ones I've seen at Loft and similar places, so may be worth a look. (Note: There is actually a changing image in that large grey space in the middle...)
Finally, this site lists various organic products and then links to the sites that sell them. Again, some similar brands to those found on sites above, and some new ones as well.
Have any others to share? (Japanese specifically, and if English sites, let me know in the comments my other post on this same topic). Also feel free to contact me, or send me a tweet.