Web manga magazines are listed here.
Comic Holic (ComiHoli)
コミックHOLIC (月刊コミホリ)
Monthly
http://www.toranoana.jp/webcomic/holic/
- Manga from this magazine is also published in tankoubon form by Fox Shuppan under their Fox Comics imprint.
Comic Seed!
コミックシード
http://www.comicseed.jp/
GanGan Online
ガンガンONLINE
http://www.square-enix.com/jp/magazine/ganganonline/
- Square Enix's free web magazine that serializes manga and light novels. The magazine started in October 2008.
Indies Comic
月刊インディーズコミック
http://mic.mangayomo.com/
- Web manga magazine that serializes original doujin manga.
MiChao!
ミチャオ
http://moura.jp/manga/michao/
- Kodansha's web comic magazine.
Web Comic High!
WEBコミックハイ!
http://comichigh.jp/webcomic.html