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/

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.