Online Reading

Animanga Network
A lot of shoujo series, along with some non-shoujo titles. There's quite a few well-known manga, and even an section devoted to Shinjo Mayu. + anime rotation

Crescent Anime
Quite a few series. + anime rotation

Dreaming Illusions
A wide variety of shoujo. + downloads

Dream-Ling
A few shoujo series. + downloads

Eirythe
Hosts quite a few manga worth reading. + downloads

Esthétique
A lot of shoujo and shounen. A bit difficult to navigate.

Eternal Enchantment
Much shoujo, some mature, all unlicensed.

Fading Memories
Shoujo. + anime downloads

Faint Memories
Some less-hosted shoujo. + raws

FairyFly
A lot of shoujo. + anime, manga rotation and downloads

Heavenly Tears
A few random shoujo, mostly scanlated ShoujoMagic, including Hisaya Nakojo's Inuyasha Peace doujinshi.

Larceny
Some less-hosted manga. + anime downloads

Marmalade Boy
Hosts the manga of the same name.

Manga Paradise (defunct)
Some less-hosted shoujo.

Mangahider
Lots of shoujo, including some lesser-known manga. + downloads

MangaVision
It's in French, but don't worry, the manga are in English. They now require registration – see a guide to registering + reading manga on the site. There's a good selection of popular manga, both shoujo and shounen. Since they're a French site, they do host manga licensed in English, but not manga licensed in French.

Misty Sensation
Mostly shorter shoujo, a few more difficult to find manga. + downloads

MOOCHI
Cute shoujo. + downloads

Ochibichan no Sekai (requires registration)
Shoujo manga. There's lots of lesser-known series, as well as some licensed titles.

One Manga
Lots of shounen and shoujo, with licensed series.

PassionCrane
A lot of shoujo and some shounen manga, with a shounen-ai division. Mostly downloads, but some series (mostly popular/longer ones) can be read online. + anime

Reconstructed Dreams
A few shoujo and shounen-ai/mild yaoi manga.

Sakura Magic
One of the oldest online manga hosting sites, if not the oldest. Plenty of shoujo.

Seraphic Tears
Requires registration for online reading, but you can download directly. Shounen and shoujo.

Shoujanga
A small site with a few shoujo series.

Silver Sea
Shoujo. + downloads

Something About You
Tokyo Crazy Paradise, Tsuki no Shippo, B.O.D.Y., and other shoujo. And Pretty Face.

Spectrum Nexus
Mainly long and popular shounen series, plus some that are rotated.

Stardust's Domain (partially down)
Shoujo, with a few licensed series. + anime & manga rotation

Surreal
Wide range of shoujo for an older audience.

Tsumi mo Nai
A few less-hosted shoujo series worth reading, plans to expand to shounen and shounen-ai.

Unrivaled Media Gallery
Hosts Death Note, FMA, Naruto, One Piece, Yakitake Japan and various artbooks.

Yurikamome
A lot of manga, many of them licensed. However there's a time limit on how long you can read. + dorama and anime downloads