In order of publication:
.hack//Legend of the Twilight
.hack//G.U.+ :http://www.mangafox.com/manga/hack_g_u/
.hack//XXXX :http://www.mangafox.com/manga/hack_xxxx/
.hack//GnU :http://www.mangafox.com/manga/hack_gnu/
.hack//4koma :http://www.mangafox.com/manga/hack_4koma/
.hack//Alcor :http://www.mangafox.com/manga/hack_alcor/
.hack//LINK Twilight Knights :http://www.mangafox.com/manga/hack_link_twilight_knights/
.hack is a multi-media franchise. The more you research it, the more you understand how it links together. Like .hack//Legend of the Twilight is a non-canon anime series and manga. But the 2 main characters are avatars of the heroes from the 4 original .hack video games. And there's an infected version of Kite that lives in the system that appears in .hack//G.U. video games, it's anime counterpart .hack//Roots, the slightly choppy manga .hack//G.U.+, and the computer animated film .hack//G.U. Trilogy.
So when you read the manga I listed, do the background check and understand at which point in time it references in the .hack world.