This is something that comes up quite a bit on forums and in IRC, so I've decided to explain it all as best as possible here. As you know, there's several different flavors of Ghost in the Shell - manga(GitS, MMI, GitS 1.5), movies(GitS, Innocence), and series(SAC, 2nd GIG). Seems that there's a fair bit of confusion as to how they all relate to each other though. Given that the movie was the first exposure for many people, they seem to take that as the canon source for everything, and thus get confused in particular about how the series can even exist(due to events in the movie). Quite simply, there's several universes that you're actually dealing with:
Universe 1 - The Manga - This is the core canon source of the whole that is Ghost in the Shell, Shirow's original works. Both the first volume and Man-Machine Interface make up this universe in a continuous fashion, and make for the base of everything.
Universe 1.5 - GitS 1.5 - Originally the sequel to Ghost in the Shell, in the editing process to collect it, Shirow scrapped this continuity which followed Section 9 after the events of the first manga. Since this did follow the first manga in continuity, I don't consider this a wholly separate universe, but since it doesn't follow with MMI, it gets to stand aside a smidge.
Universe 2 - The Movies - As said, this is probably where most people know Ghost in the Shell from, and thus come away with their assumptions of what Ghost in the Shell entails. So far as I'm concerned though, this is the least GitS-like of the GitS universes, being directed by Mamoru Oshii, who has a rather different approach to things than Shirow(not that this is necessarily bad thing, Oshii's a solid director in his own right). Both the original movie and the upcoming(oustide of Japan anyhow) Innocence follow in Oshii's vision of the Ghost in the Shell universe, with some events in the first movie reflecting similarly on the first manga.
Universe 3 - The Series - The most recent of the GitS universes, SAC and 2nd GIG feel a lot closer to the original manga than the movies, but still follows in its own separate, more serious, universe. The biggest indicator that things are different is the use of Tachikomas instead of the Fuchikomas in the manga. Additionally, the storyline(s) in the series are wholly new, with writing help from both Shirow and Oshii, among others. One of the initial announcements for the series basically said "here's Ghost in the Shell as though the Puppetmaster incident never happened."
Other - The Games - I figure I should mention the two GitS games here as well. The original Playstation GitS game, as far as I'm concerned, falls into a period within the timeframe of the first manga, as it makes use of the Fuchikomas, has a very similar art style, and doesn't do anything that clearly violates continuity. The SAC game on the PS2 seems to follow similarly, things appear close to the way they are in the show, and it doesn't do anything obvious to break continuity. There is also an SAC PSP game in the works, but as it is still early on in development, I really don't know much about it at this point.
Given these different continuities, much happens differently, but there are still elements that cross over from one universe to another. In most cases, its an element from the manga being found somewhere in the movies or show, but in some instances they originate elsewhere. Because of the nature of it, I'm going to start from where things show up the second time and then tell you where they come up originally. Additionally, there's some elements drawn from Shirow's other universes and I'll point out those that I noticed.
- Dominion's Annapuma and Unipuma show up while Motoko's investigating the Geofront in Chapter 07 Phantom Fund, sidetracking her Fuchikoma with their sales booth.
GitS 1.5 - None that I can find.
GitS 2: Manmachine Interface - Again none noticed.
- Overall plot follows that of the manga's Puppeteer storyline, renamed to the Puppet Master for the movie, but decidedly shortening the period of Motoko's fusion and abandonment of her shell.
- The opening sequence mirrors that at the very start of the GitS Manga, slightly altered to include Nakamura.
GitS 2: Innocence
- The basic plot draws from Chapter 6, Robot Rondo, where sex androids start going berserk and killing their owners, and Section 9 looks into the cause.
- Like at the start of Robot Rondo, Batou takes out a berserking android with a pair of high powered gloves and leaves it for the cops to clean up.
GitS: Standalone Complex
GitS: Standalone Complex 2nd GIG
GitS: Standalone Complex (PS2)