These are what I found online both Main stream and Indie Brands.  If you would like to add more please feel free to comment. 

6%DOKIDOKI
Alice Auaa
Algonquins
Angelic Pretty(Japan)
Angelic Pretty (USA)
Anna House
Atelier Boz
Atelier Pierrot
Baby, The Star Shine Bright
Beth
Black Peace Now (BPN)
Body Line 
Candy Fruit 
Candy Violet
Choco Chip Cookie
Coquette Doll
Cute Plush
Deep Forest
Despair
Emily Temple Cute (Kyoto) 
Emily Temple Cute (Osaka) 
English Charm
Ergi
Excentrique
Elements
Fairy Wish
Fan+Friend
Girlie
Gloomth
HeartE
HellCatPunks
h.NAOTO
ID-Japan
Innocent World
In the Star Light
Jane Marple
Jelly Bean
Juliette et Justine
Junks
MA/MAM
Mari's Rock 
Marble
Mary Magdalene
Merry Bell
Metamorphose temp de filles
Miho Matsuda
MFashion
Mille Fleurs 
Milky Ange
Miwitch
Moi-meme-Moitie
Na+H
NingYouDou
OhmatiPrison
Pina Sweet Collection
Princess Doll
Putumayo
Seraphim
Sex Pot Revenge
Suppurate System
Shirley Temple
Sweet Rococo
The Gabriel Chelsea
Triple Fortune
Union Jack
Victorian Maiden
Visible

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Korean Lolita Brands update 05/09/2011

Baroque

Dolly Berry

Goth Loli Closet

Mew & Lief

Snow White

Apricot

Milk

http://www.milk-web.net/

Swimmer

http://www.swimmer.co.jp/

thanks zeruda, swimmer is definitely good!

I absolutely love Swimmer.  ♥___♥

i found a brand in japan called Harajuku Angel, althought that could have just been the store name but Idk

@abelana: do you know if it has a website?

i donno it was a small shop in the Harajuku district

is there an easier way to buy from bodyline? i can not understand the forms

@Do-chan: Bodyline is a shopping cart then, pay through paypal (or credit card) method.  I don't understand what you mean by forms? 

my biggest problem is i cant see the names to choose a state and it wont accept my zip code