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.
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.
While Batou is in the Grocery Shop, as a hooded character walks past Batou, a voice tells him "You have entered the killzone"; many speculate the character is Motoko Kusanagi. In fact, in the 'special features' on the DVD, which documents the making of Innocence, Atsuko Tanaka (the voice actor for Motoko) is shown during one scene to be recording precisely that line in the studio. It therefore seems that the voice was indeed Motoko, Batou's guardian angel, warning him of Kim's impending hack of Batou's brain right there and then.
A co-production with Studio Ghibli. Production I.G. president Mitsuhisa Ishikawa personally asked Ghibli president Toshio Suzuki to co-produce, as the projected budget of 2 billion yen ($20 million) was too much for one studio to handle.
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".
One of the minor characters, forensic analyst Ms. Haraway, is a reference to the real-world professor of sociology and biology, Donna Haraway, who is a stern contributor to the whole transhumanism, post-cyberpunk movement. She has been quoted as saying that "I'd rather be a Cyborg, than a Goddess", in reference to her firm belief that in order for women to really liberate themselves from a "patriarchal society", they should devote themselves to technology and its applications and become cyborgs, as a means of separating themselves from men, and the common misconception of "what defines a woman and a female", including the stereotype that what defines a female as a woman is her decision to bear children. Ms. Haraway in the films has no children of her own, and does not facilitate or even comprehend the emotional content that comes with bearing a child; she thus has a rather harsh feminist outlook on child-rearing and childbirth.
Batou's access code for his car is 2501, the same number of the Puppet Master. In the first Ghost in the Shell movie, this is the recognition code agreed on between Motoko and Batou after her fusion with the Puppet Master and before she disappears. In Innocence, this is how Batou recognises that the infinite loop he and Togusa are experiencing in the Doll House is a trap - Motoko slips him clues in the hallway, one of which is '2501'.
When Batou and Togusa are exploring Kim's mansion, Batou finds a figure that resembles Motoko Kusanagi's appearance from Ghost in the Shell (1995), 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.
Batou is twice referred to as an elephant in the forest. This is an allusion to a Buddhist poem: "It is better to live alone; there is no companionship with a fool. Let a person walk alone with few wishes, committing no wrong, like an elephant in the forest."
A real music box was used to create the music for the Doll House, using an 80-note disc-playing (as opposed to drum-playing on typical music boxes) machine called "Orpheus", manufactured by Sankyo Seiki of Japan. The music box was played and recorded in the studio; the recording was then taken to the Oya Stone Museum (a former subterranean stone quarry) where it was played back over a 5.1-speaker setup and re-recorded. The reverberation thus introduced was to mimic the vast expanse of the Doll House in the anime.
Locus Solus seems to be a Cantonese outfit - the control robots of the factory ship's systems all communicate in Cantonese, and presumably so do the staff (the announcer over the ship's PA system, instructing the security teams to arm after the gynoids start activating themselves, speaks in Cantonese).
Mamoru Oshii: [Basset Hound] 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.