While I am also a fan of the excellent Ghost In The Shell manga and film (which, if you're not aware were huge conceptual and visual influences on The Matrix ), the Stand Alone Complex TV series, especially season 1, gets the most repeat viewings from me. The SAC stories revolve around Section 9, a branch of high level government cyber cops, most of whom are artificially enhanced, i.e. cyborgs with computer augmented brains. It's more of a high tech cop/action series than a philosophical exploration of humanity that was the heart of the original manga and film but manages to be one of those rare cases where the sequel gives fans what they want - in this case more action and more Major Motoko Kusanagi - without degrading the high standards of the original work.
Season 1 is made up of "stand alone" episodes, single one shots that usually explore the personalities of a member of the Section 9 team in a bit more depth, and "complex" episodes, which deal with a cyberterrorist called The Laughing Man. The episodes are well-paced and find clever ways of interweaving plots, even where the "stand alone" episodes are theoretically not dealing with the extended "complex" story. For the lit-nerd, characters quote Holden Caufield casually, sly Salinger references appear in the backgrounds and, of course, "The Laughing Man" is directly from the story of the same name.
Also of note is the excellent score by Yoko Kanno, which while all over the musical map stylistically, is a terrific and strange but always compelling. Progressive metal bumps up against percolating techno and Asian pop one minute, Western action film music breaks though in the next, it's nearly as terrific as Kano's score for Cowboy Bebop.