Big Lipped Alligator Moment: No information is ever given about Proto in the few appearances he makes in 2nd Gig. It isn't until he falls victim to an attack barrier and reveals that he's a Bio-Android prototype that we ever learn anything. Unfortunately, this comes near the end of the series, and really plays no part of the story, and such a detail was never hinted at or mentioned again. It may have been an Aborted Arc that somehow still got some details through, or a possible Sequel Hook for another plotline.
There was one small hint. Proto is short for Prototype.
NIGHT CRUISE is an entire Bizarro Episode, even considering the series' other Stand Alone episodes. Other than a quick conversation between Section 9 off-handedly tying it to the Individual Eleven arc in the last couple of minutes of the episode, it serves no purpose other than being a Whole Plot Reference to Taxi Driver, and Section 9 barely even shows up.
Complete Monster: Kazundo Gohda is the director of the Cabinet Intelligence Service. A smug, charmless, callous, and amoral Manipulative Bastard, Gohda's (largely self-inflicted) Inferiority Superiority Complex and obsession with Great Man theory led him to kill hundreds with the terrorist-producing Individual Eleven virus, come within inches of starting a genocidal war, and try to nuke a crowded city-state half a mile off the coast of Japan just to show that he could. To give some impression of how severely he eclipses the other villains of the series in heinousness, one of his minor crimes was deliberately exposing labourers to a dangerous work environment (he asked them to excavate a buried ruin, but didn't tell them it was a heavily-irradiated nuclear facility), and then covering it up with a string of murders. Someone else did something similar on much the same scale elsewhere in the series, and it became the driving force of most of the first season.
Faux Symbolism: Batou struggles under the burden of a massive steel cross as he tries to save the Major at the end of 2nd Gig. Furthermore, this shot is immediately following a line that suggests he is the one person she can open up to.
Not long before that, when Kuze reaches his hand out to the Major, the bullet holes in his hand only serve to underscore the Messiah role he seems to be taking up.
And the Major gives Kuze an apple. Way to mix your Biblical metaphors, guys.
The scene in BARRAGE (episode 25 of season 1) where the Tachikomas hear the Major's voice encouraging them and the audience is shown a close-up of the Kannon statue on her estate. Conveniently for Western viewers, it could also be seen as a statue of the Virgin Mary.
If you were wondering who the identity of the fifty-ish looking man with important knowledge of The Laughing Man was in the "Chat" episode of season 1, pay close attention and you'll notice that he and TLM share the same VA, Steve Blum (with each at opposite ends of his vocal range, no less) meaning they may well have been the same person.
Kuze claims to keep his face frozen and emotionless to keep it "perfect". This makes sense when you consider that his long lost childhood crush was not only The Stoic, but introduced to him waving off a doctor who was "helping" her smile.
Growing the Beard: While the first season is still good, 2nd Gig could be considered an improvement, with more episodes tying into the overarching plot, including the "stand alone" episodes (even the infamous NIGHT CRUISE episode,) delving into the Major's backstory (and at the same time giving the main conflict more of a personal meaning) and with a more satisfying ending compared to the more anticlimactic ending of the first season. The Major also starts wearing pants.
Memetic Mutation: The Laughing Man logo. This is an extra special meta meme, since the Laughing Man arc is partially an exploration of memes in the traditional sense, with the Laughing Man coming to represent a meme with no clear origin.
Mood Whiplash: The Tachikoma shorts. Full. Stop. It can be pretty jarring to go from a serious science-fiction police procedural to a bunch of cutesy, blue tanks goofing around with each other.
Narm: From the English dub of Episode 6: "NOW THE PURGE WILL BEGIIIIIIIN!"
Not to mention the episode's title is "Meme", albeit used in the Dawkinsian sense.
Paranoia Fuel: If you think about it, you can be hacked at any time, by anyone, to force yourself to commit suicide, murder your family, reveal personal secrets... There's a reason why some people refuse to have any cyberization in their brains at all, despite the disadvantages: it makes their brains effectively hack-proof. There's one case of an extremely reclusive rich guy who is paranoid of anyone stealing his secrets, and has no brain-jacks at all, so Section 9's usual method of digging up cyber-dirt on their subject is stymied.
The Tachikomas are usually pretty adorable, but when we see them being stealthy, it's a bit unsettling. They're invisible, nearly silent despite their bulk, can fit into surprisingly small spaces, and can climb walls and ceilings. A freaking tank could be stalking you and you'd never notice.
The Problem with Licensed Games: Mostly averted in both the PS2 and PSP spin-off games. Both games have plenty of character interaction that you'd expect to experience from Section 9's members, and has deeply fleshed out storylines and dialogue that tie neatly into the SAC universe as Stand Alone episodes. Connections to the Nemuro Landing Operation in particular for the PS2 game. The problems are that they're technically mediocre, featuring loose Run-N-Gun controls, difficult platforming, fair graphics (for 2006-era games), cheap AI, and downright horrible music that usually consists of a few boring notes looping every 30 seconds or so. They're faithful to the series' established lore and storylines, but aren't presented in the best fashions.
Uncanny Valley: Kuze is more than likely an intentional example, since his face is constructed in such a way that he remains utterly stone-faced throughout most of the show to the point of rarely even opening his mouth to speak.
What Do You Mean, It's Not Political?: The anime was created and aired during both terms of the Bush administration, but making an imperialistic version of America as the villain is not supposed to be a shot at either America or Bush's policies. The premise dates back to Shirow Masamune's Appleseed series, which he wrote before Ghost in the Shell in the early '80s.
While the concept may be derived from a much older work, it's hard not to see Kenji Kamiyama's choice to use this particular idea for the series in light of the wave of anti-American sentiment sweeping the international community during the mid-Bush years when both seasons were made. Kamiyama seems none too fond of capitalism either. What makes all this particularly ironic is that the series was partially funded with American and British money (Bandai USA and Manga Entertainment, specifically).
The Laughing Man and the social phenomenon he inspires bear distinct similarities to Julian Assange and Anonymous, respectively. However, the series was made several years before Anonymous popped up, and several more years before Assange gained international notoriety, making the first season come across as bizarrely prophetic in hindsight.
It's hard not to see the similarities between Hideo Kuze and left-wing revolutionaries such as Che Guevara (the Major even explicitly compares them at one point), plus the similarities between his vision of the "superstructure" and a socialist utopia. That the second season's other (far less sympathetically portrayed) villain is a right-wing bureaucrat who has a close working relationship with the imperialist Americans and is jonesing for a return to Japan's Cold War economic golden era is also somewhat eyebrow-raising. America has also been portrayed as an openly imperial power that conducted an openly imperialistic invasion of Mexico in the series. This does tend to fit the usual leftist narrative that describes America as an evil imperialistic capitalist super power.
Kuze is also compared to Malcolm X and Cassius Clay (a 19th century abolitionist). What they all have in common is that they were highly controversial, morally gray liberators, whose true achievements still remain a matter of debate. Kuze's ideals are repeatedly called a "delusion", even by people who willingly follow him. It's supposed to remain ambiguous how good answers he actually has to the very real problems he presents, and how much is just people being influenced by his enormous charisma.
Take a good look at this map◊. The Russo-American Alliance is basically the Democratic base, plus Arizona. The United States of America encompases several swing states and the American Empire is built on the states which used to form the confederacy and currently the Republican base.
The Woobie: The Tachikomas in the English dub are this, but only sometimes. When they're only talking, they become The Woobie because of their adorable voices, but when they're fighting the Woobieism changes and they become both an Iron Woobie and Badass Adorable at the same time.
Prime Minister Kayabuki might also count for some viewers. The poor woman could really use a vacation...
Woolseyism: Since a lot of characters speak without opening their mouths, there's more room for this than in most productions. The dub usually strays really close to the subtitle's translations, but there are a few times when some minor improvements are snuck in. A notable one is when Batou sees a rich man's collection of expensive cars and remarks, "What a shame." The dub inserts the line afterward, "All these beauties in captivity, when you should be running free in the wild." Entirely in-character for Batou, and funny to boot. Another is when a Tachikoma is shot to pieces on a highway by a tank they're pursuing; its brain is fine, fortunately, and the Major tells it to sit tight. The dub adds the line "Sure thing... since I can't move..."