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Marmite isn't a manga, at least originally, but it did pretty much lay the groundwork for yuri in the 21st century. A little something beyond smut and dead lesbians.
Beyond that, while it's more well-known for its anime adaptation, Kannazuki no Miko, among the other '04 heavyweights are the cross to Marimite's jab for yuri's big one-two. Big watershed moment of yuri in otaku media. If not full blown yuri, at least responsible for the rise in use in yuri subtext and yuri elements as a viable allure for audiences, rather than just something the staff/author put in because they like yuri. That is pretty much /u/'s daily bread and butter.
