The music-box tune in Kim's mansion was actually recorded in a large outdoor space, because the sound engineer wasn't sure if he could alter the music electronically to have an authentic feel in 5.1-channel surround sound.
When Batou and Togusa are exploring Kim's mansion, Batou finds a figure that resembles Motoko Kusanagi's appearance from Ghost in the Shell, along with a row of numbered cards reading "2501". In the original Ghost in the Shell, Project 2501 was the code name given to the Puppet Master project and became the code Batou and Kusanagi agreed to use when they wanted to contact one another.
Much like how the original Ghost in the Shell movie used scenes and stories from several issues of the original manga (specifically issues 1, 3, 9 and 11), Ghost in the Shell 2 was inspired by issue 6, "Rondo".
The opening sequence shows two cybernetic bodies angled so as to show two pairs of legs joined at the hip. This is a reference to the doll sculptures created by the German surrealist Hans Bellmer in the 1930's, and at one point in the film a book by Bellmer can be seen.
Director and Writer 'Mamoru Oshî' put a basset hound in the picture because he is a fan of the breed and owns one himself. He makes a reference to his own basset hound, Gabriel, in the scene inside Batô's apartment where the dog figurine plays music.