There are two sources for the title of the show. The first is the text at the beginning of the first episode, where it describes the psychology of some of those without cybernetic implants. Essentially, they have a "Stand Alone Complex"; they feel that they "stand alone" from the rest of humanity who have cybernetic implants, which allow those with them to communicate at any time with anyone who also has implants. The second source is a reference to the story itself. The term is used to describe an event where multiple people who have no associations with each other and are not part of a common group(thus they "stand alone"), through similar actions, seem to work together towards a common goal. This "complex" is referenced a number of times in the story, mainly about the laughing man case, but also in reference to a few other cases the group encounters.
The text revolving around the Laughing Man's logo reads: "I thought what I'd do was, I'd pretend I was one of those deaf-mutes." This is actually a quote from J.D. Salinger's classic novel "The Catcher in the Rye"; additionally, the Laughing Man's name comes from a short story of the same name by Salinger.
In the "Tachikoma Ready-Room" you can sometimes hear a faint noise. It's the familiar computer sound from the old Viaje a las estrellas (1966) series.
In the first episode, "Section 9," during the scene where the foreign minister tries unsuccessfully to read the stolen report, the camera zooms in on one of his cybernetic eyes. Amongst all of the usual symbols and jargon you'd expect on a camera lens, the words "Directed by K.K." can be seen. This is a reference to Kenji Kamiyama, the director of the series.
Sometime, the drawing director is different for each session, so you'll find major. Motoko Kusanagi is a little different in each session .