Ghost in the Shell

// Explaining GitS: SAC

Ghost in the Shell SAC is complicated, but much can be understood with rewatching and independent research. Here, I'll just mention a few storyline items that have particularly baffled some viewers. *TONS OF SPOILERS AHEAD*

// Who is the Laughing Man?

We can break this identity down into three groups.
1. Aoi is the young man in a blue hoodie who stages the infamous kidnapping Serano incident that gained the nation's attention. He is a master hacker who is able to hack the eyes of a large amount of people as well as tv channels, all in real time. Aoi crosses paths with Section9 numerous times, and is considered the main Laughing Man in the TV storyline. It is important to note, however, as Aoi himself states, that he is not the original Laughing Man.
2. Copycats & imposters appeared after the famous hostage incident that Aoi conducted. Many corporations staged fake Laughing Man pranks to claim they were being blackmailed, and to collect money from the government. Fans who copied the Laughing Man did so due to the absence of their hero. This is confirmed in Ep 9 Chat! Chat! Chat!.
3. The Original Laughing Man remains elusive. He is the one who first discovered the corruption at Serano and wrote the original email blackmailing the company. It would be Aoi who accidently discovers this data, and actually executes the plan. At the end of the series, he makes a brief appearence around the Serano CEO, showing he's still around and watching. His only line refers to how we must adapt to survive.

// How did the Major survive that shot?

In Ep 25 Barrage, the Major is seen to be assasinated through a sniper shot to the head. Her head is completely blown off as her body falls to the ground. In Episode 26 Stand Alone Complex, she shows up alive and well. How did she do it?
1) She was remote controlling that body. Motoko has strong survival tactics, and a fondness for using remote bodies. She does this in Ep 22 Scandal in the hospital, and in Ep 25 Barrage with the young girl Motoko body saving Batou (nice homage to the movie, btw). It is likely that she would have been walking around in an empty shell knowing that Section9 was being hunted. It's like a body double. Note that in the last episode, she was shown in the same old body she injured previously.
2) She uploaded herself to the net. In the last episode, Aoi comments that he was concerned Motoko would be wandering the net forever, not wanting to come back to the physical world. It could be that, sensing the danger she was in, she uploaded her ghost to the net, before her body was shot. This is the same thing the Major did in the original 1990s film.
Either way, do note that during her assasination, she was not wearing her watch, despite having received it again recently. This means she was aware of her situation, took preventative measures early on, and left her watch in a safe place, since it was not safe on her present body.

// What did the ending car click mean?

It's the end of the first season. Aoi has been uncovered as the Laughing Man, and everything seems wrapped up and dandy. NOT! Serano CEO walks to his car, attempts to opens the door, and click! Serano gasps, something happened. We see the original Laughing Man walking away... What happened?
Here are a few possibilities.
(1) The original Laughing Man brain hacked Serano. His plan is not yet over, and Serano is not being let go of that easily.
(2) Laughing Man unlocked/locked the car. Just a reminder, or even a warning, that he's still around watching these events unfold. He's always one step ahead of everyone else. or
(3) There's a bomb in the car. Serano didn't keep his promise, and the Laughing Man will not let corporate corruption go unpunished.
Since there's no official word on it at the moment, it's left up to you, the viewer, to decide which interpretation you think best fits the story.

// Why aren't more concerned about brain hacks?

From the perspective of the viewer, it seems like people are brainhacked all the time. Why people don't go to autistic mode more, disconnecting themselves from the web and possible danger?
It only seems common because the show focuses on cyber brain crimes due to the nature of Section 9 and the sensationalism of the tv series. Brainhacking skills among the population are actually fairly uncommon. Motoko, Batou, and the others are extraordinarily skilled in brain hacking. They are, after all, in an elite intelligence agency and have state of the art equipment.
A good comparision would be, why do we shop online when we risk identity theft or credit card theft? Because the number of thefts that occur are relatively small compared to the number of online transactions that go on everyday. Why do we drive cars when we might die in an accident? Because driving is a large part of our lives, and the likelihood of a fatal accident for any given drive out is fairly small. Likewise, people in GitS are not concerned with brain hacking as it's an infrequent crime.