Now the disclaimer: everyone has different standards for what they call "clean." These companies meet my standards or higher. Also, I have not researched each of these companies personally, so before you buy any product, you should check the ingredient list (always) to make sure they aren't using anything that you don't want on your skin or in your body. Also, I still recommend checking any product with the SkinDeep database at safecosmetics.org as always.
Ok, so here you go!
100% Pure
Alteya Organics
Aubrey Organics
Avalon Organics
Baby Bear Shop
Badger
Bubble and Bee Organic
Burt's Bees
Dr. Bronner’s Magic Soaps
Desert Essence (only the Organics line)
Earth Mama Angel Baby
EvanHealy
Griffin Remedy
Gabriel
Hugo Naturals
Indian Meadow Herbals
Intelligent Nutrients
Jane Iredale
John Masters Organics
Larenim
Kimberly Parry Organics
Little Angel
Mercola
Miessence Certified Organics
MyHoneyChild
Nature’s Paradise
OGmama and OGbaby
Organicare
Organic Essence
Origins Organics
Purely Shea
Rose Tattoo Aftercare
SoCal Cleanse
Sensibility Soaps/Nourish
Terressentials
Trillium Organics
Vermont Soap
Zuzu Luxe (a division of Gabriel)