There's some brilliant characterization in the second episode between Falcone and Mooney that needs a second go to recognise. Mooney isn't angry with Falcone for beating up her boytoy - she's angry at him for humiliating her in front of her power base. Her words to Falcone to try and get him to back off (really, a "I wouldn't consider Lazslo important") and her immediate scream to get all witnesses out after the deed is clear evidence of that. This also explains why she gets rid of Lazslo post-haste; why keep evidence of that humiliation around? Falcone also knew exactly what he was doing. Mooney hasn't actively been disloyal, and he surely knows all his subordinates want to get rid of him - he's not an idiot. But he needs to keep her in line. He explicitly asks her to keep everyone in the club to watch her public humiliation. The whole beating was a demonstration of his power to an underling - "Don't talk shit until you can stop me from walking into your place and breaking something important to you."
While Alfred's staunch refusal to take Bruce to a therapist is rather necessary to maintain canon, it also makes sense in the scope of Gotham's world. Supercriminals are almost all criminally insane people who never get better for their stays at Arkham Asylum, which itself becomes a haven for criminals and mad scientists. We see another therapist is hypnotizing her clients to become serial killers. In this world, therapy at best simply doesn't work, and at worst drives people even more insane. Alfred is quite right in keeping Bruce away from those dirty headshrinkers!
During "Viper", Bullock throws back "What's altruism?" to a professor conspiring with a chemist looking to expose a weaponized toxin to the world. While Bullock may be asking the question thinking it's a vital clue to the case (it does give Gordon a "Eureka!" Moment), he's genuinely flummoxed by what the word means. It's a sign of how corrupting and corrupted the city of Gotham has become...
Why was Barbara unable to tell the girl she spoke to on the phone was a 12 year old girl and thought Gordon was sleeping with another woman? Because she herself just cheated on him. So of course she would suspect someone of doing something she did herself.
Falcone breeds chickens. He also took Oswald Cobblepot under his wing as his new mole inside the Maroni family, who will also help him deal with Fish Mooney. He appreciates Cobblepot as a fellow scheming mobster, and their shared respect for Gotham City - they'd both rather be running a vast criminal empire within its social order than see the whole thing slide into chaos. He even tells Cobblepot as much when he's tending to his chickens. "The Penguin" is symbolically another bird he is rearing.
Edward Nygma working in the forensics department. This means his job is examining everything for possible clues that may help solve the crime. And what is the Riddler's modus operandi in many continuities? Laying out clues for his own crimes, for Batman to examine them! In the comics he also had a stint as a semi-legitimate private detective at one point. This Nygma could definitely pull that off if he wasn't destined to become a criminal.
Falcone having two of the future 'freaks' in his employ shouldn't be that surprising. After all, while in The Long Halloween he says that the mob has a policy to not work with them, he says it to Poison Ivy after paying her for a job she did for him, and continues hiring them for oddjobs his men can't do...
The whole "Spirit of the Goat" thing makes a little more sense if you know that "Gotham" means "goat home".
In "Under the Knife", Alfred questions Bruce having invited Selina to a charity ball, and Bruce, not wanting to tell him she'll be helping his investigation, plays along with Alfred's assumption that Bruce is crushing on Selina. All very pre-teen and innocent, and all they do is dance while they look for the man Selina needs to pickpocket ... but was this pretense of a "date" the first inkling of Bruce's future "playboy" facade?
The revelation in "The Hammer or the Anvil" that Selina's murder of Reggie was utterly pointless can be seen as reinforcing Bruce's (and future Batman's) Thou Shalt Not Kill philosophy. Even if Reggie had told Banderslaw what Bruce was investigating, all that would have resulted is Banderslaw giving Bruce "The Talk" in different circumstances, so the end result would have been the same. Killing Reggie ended up doing nothing except making Selina a killer and Bruce somewhat of an accessory.
At the very end of "All Happy Families Are Alike", Bruce learns Thomas' secret - the Batcave. This is in a way, a neat reference to the idea of Thomas Wayne being The First Batman, as depicted in the classic Silver Age story of the same name - much like how Bruce, in that story, was sub-consciously inspired by his father's bat-costume to create the identity of Batman, Gotham Bruce will be inspired by his father's secret work in the cave (most likely investigating the corrupt elements within Wayne Enterprises) to launch his own war against crime and corruption.
Symbolizing the fact that Batman has generally been portrayed as having a distinct technological advantage over most people, when Bruce and Alfred break into Thomas Wayne's hidden office and the Cave they find that sitting on the desk is a flatscreen monitor and computer keyboard, which is revealed to be connected to a server stack. The Schizo Tech aspect of the setting has previously shown that displays, even the TVs of a mega-rich family like the Waynes, were old fashioned cathode ray tubes, and personal computers before Season 2 were nowhere to be seen (and the ones eventually seen, aside from the ones in the Cave, also have old-fashioned CRT displays).
David Mazouz, as a young teenager, is undergoing a growth spurt and the show is using it. In the pilot episode he's directly adjacent to Ben McKenzie so you can see how small he is and how vulnerable Bruce Wayne must be. In "Damned If You Do", the premiere of the second season, he's again in physical proximity to Gordon but this time getting closer to him as a physical equal while also being more confrontational.
While obviously horrible, the Maniax murder of most of the GCPD will have a positive aspect, as it removes most of the corrupt and/or scared cops that were willing to leave Gordon to die last season, "cleaning house" as it were. Most of the resulting new blood that have the guts to join the force after that will do so out of a sense of altruism like Gordon and many of them will probably end up looking up to Gordon as a senior surviving officer and possibly some of them even being trained by him. Thus this will greatly help facilitate Gordon's eventual rise to Commissioner.
While the death of Jerome takes away a character who truly embodied the Joker, the idea that he inspired others so that the character is less a specific person but rather a meme or ideology does work with the mythology. The Multiple-Choice Past? Different people who take up the mantle. The utter unpredictability and methods so he might be a mostly non-lethal prankster one time but a brilliant mass murderer later on? The personalities of those different people. Joker Immunity? Kill the Joker and someone else takes up the identity. You can never get rid of the Joker.
The Riddler is normally described as having some sort of compulsive need to leave clues due to an unspecified mental issue. This version of Edward Nygma is being given another reason: he's an adrenaline junkie. Nearly getting caught but getting away with it gives him a high, and how better to ensure that you run the risk of getting caught than leaving clues to your crime? This conveniently explains why he becomes obsessed with Batman; because Batman takes away the "getting away with it part", Nygma can't get his high. He's a junkie being denied his fix.
According to Barnes, every man can do anything in the right situation, and his proof is how he once shot a tied-up insurgent to prevent him from escaping, but when Gordon finds himself in the same situation he doesn't pull the trigger. Sounds familiar, even if Joker's not involved.
Barbara's injuries after her fall include a concussion. This, conveniently, provides a way out if the future of the series eventually has Jim marrying Barbara. After all, a brain injury is a traditional comic book method of causing an altered personality.
Bruce's interactions with Gordon, Selina, and the rest of the future criminals and freaks of Gotham might seem a bit of a stretch, especially since none of them later figure out his secret identity, but knowing young Bruce Wayne would make them even less likely to suspect him of being Batman. To them, he's still the vulnerable, idealistic boy whom they've had to rescue on several occasions, making him a very unlikely candidate for the masked vigilante!
Even later in the series after Bruce takes several levels of badass, having his true character known by multiple characters still works, because everyone who knows Bruce well enough to guess at Batman's identity in the series finale likes him enough not to turn him in and/or approves of his unusual career choice. Interestingly true of even the two villains (Selina/Catwoman and Jeremiah/Joker) who were friends with him before he was Batman. They both guess who is behind Batman's mask immediately, even though Bruce's face is covered and they haven't seen him for ten years, and neither of them seem to even consider telling anyone. Justified, since Selina is still Bruce's friend and Jeremiah...at least thinks he is.
Bruce seemingly getting inspiration from Azrael which he will later use to develop the look of Batman adds a level to the original "criminals are a cowardly and superstitious lot" rationale from the original stories. Being scared of a guy dressed like a bat? Maybe. Being scared of someone who looks a bit like that axe-crazy lunatic who was running around a few years back who had come back from the dead? That makes a great deal more sense.
Why didn't Jerome immediately resurrect after Dwight electrocuted him? Well, earlier Lucius mentioned that the body core temperature had to reach a certain level, but Jerome's skin was noticeably still tinged blue with cold during the attempted resurrection. Later, when he revives on the morgue table, his twitching hand is back to a normal color, indicating maybe he just needed to thaw more first.
Jerome complaining when Bruce blindsides him and takes him to the floor asking what kind of "hero" does that perfectly demonstrates Batman's future method of operation: Combat Pragmatist and Good Is Not Dumb. As well as the Joker's constant complaining that Batman cheats.
Penguin putting the Riddler in stasis thanks to Mr. Freeze provides a convenient way to deal with one of the issues raised early on with the series: in the comics, the Riddler is roughly Bruce Wayne's age, but with Nygma already being a CSI when Bruce is still 12 years old, he'd have to be at least 10-15 years older, if not more. Being frozen explains how that could still happen: he gets thawed out at some point after years have passed while Bruce ages normally, bringing them closer in physical age.
The Riddler only gets frozen for a few months, so it doesn't work.
Some people have complained that having a Lazarus Pit directly under Gotham seems pretty contrived, and misses a great opportunity to have set that scene overseas. But if you consider it from the Big Bad's point of view, it makes perfect sense: in this iteration of the Batman story, Ra's al Ghul probably only became interested in Gotham City in the first place because such a Pit was down there. Everything else about the Court of Owls and his seeking an heir in that particular city is a side-effect of him keeping tabs on that resource.
Fridge Tear Jerker: Alex's father loses his father and his son in quick succession, both to the same man, and one who we know is virtually guaranteed to either escape justice entirely or, at best, to be killed under circumstances that can never be fully made public. And he didn't actually need to kill either one of them.
Butch's season four reappearance as Solomon Grundy lasts for seven episodes: the same as the number of days and events referenced in the "Solomon Grundy" nursery rhyme. He'd "born" on the first episode/Monday and is "buried" by the re-emergence of Butch's identity on the seventh episode/Sunday.
Bruce's descent into drunken Jerkassery in season four is a pretty serious departure from the established Batman mythos, but when Bruce finally becomes Batman, the reputation he's generating is going to work very well in favor of maintaining a secret identity. The greatest nightmare that Gotham criminals will ever know is really this self-destructive twerp? No one will ever believe that.
Fans' sheer disbelief that Bruce would reject the people who really care about him - Alfred, Jim, Selina - to hang around with a bunch of degenerate rich brats you'd think he wouldn't even like are missing the point: he's hanging around with such jerks precisely because he doesn't like them. Because the last villain he confronted while trying to be a hero threatened everyone he loves, and the last nice person his own age whom he'd let himself feel empathy for (Alex) got his throat cut. Bruce is screwing around with people he doesn't give a damn about, because he wants to not have to give a damn if they get hurt or threatened, too.
In a roundabout way, Bruce is still responsible for the Joker's creation, as if he killed Jerome in The Gentle Art of Making Enemies or let his uncle kill him in One of My Three Soups, he would never have been able to give Jeremiah the laughing gas that would drive him insane.
In a nice touch of Fridge Irony, the Joker is "born" on Bruce Wayne's birthday. Worst. Present. Ever...
The twist of Jerome having a brother who is the real Joker makes sense when you consider that every deck of playing cards comes with two Joker cards.
The writers have neatly managed to incorporate multiple variations of the Joker in Jerome and Jeremiah; the sociopath who was essentially born bad, the good man who had One Bad Day and went crazy, the ones with ordinary skin but wears makeup, the version with his face stitched on, the classic white-skin and red lips, the one hired by others for their own schemes but who they lost control of, the axe-crazy lunatic, the careful planner, and one born due to the actions of Bruce/Batman. They didn't end up creating a Gothamverse version of a Joker, they've created a version that incorporates almost all the versions of the Joker.
Bruce Wayne showed respect towards Jeremiah and his genius, and felt it could do good for the world. This could be an in-universe reason for why Bruce won't kill Jeremiah/Joker when he is Batman, as he will still have hope that he can cure Jeremiah and bring him back to the good side, as he saw what potential he had before his brother messed with him.
It also gives the Joker an origin closest to Batman's own of all the villains shown so far. The Penguin worked his way up through the mob. The Riddler had a mental problem that slowly took him over. Firefly had been engaged in crime with her brothers before she was experimented on, Mr. Freeze had been experimenting on innocent victims before Hugo Strange got him, Hugo Strange was bad for a long time, Poison Ivy choose to become selfish and self-absorbed even before she received her final power-up, and even Selina was a street kid and petty thief. Despite his background, Jeremiah was living a law-abiding life, had found success, and with his brother dead could live a normal life without fear, and then one day it was all taken away from him and he was broken, just as Bruce's good life was taken from him and he was broken in one night. In this continuity, the Joker really is Batman's counterpart, and Bruce may be afraid that if the Jeremiah is forever lost because the Joker is irredeemable, than what does that say about him?
It also brings shades of Two-Face's dramatic motif into the series, despite Gotham being set too early to plausibly incorporate that particular Rogue in its Gallery of villains. Harvey Dent is still too low-ranked in the district's legal profession for his Start of Darkness to be addressed, but making Bruce feel empathy and regret for Jeremiah's gas-induced descent into insanity provides a substitute for Batman's traditional relationship with his disfigured and mentally-ill former friend and DA ally.
After accidentally shooting a fellow officer Harvey makes a very subtle change to his M.O. in response. His revolver holds 6 rounds yet, when he enters a shoot-out with Jim while under Ivy's influence he is clearly reloading after 5 shots. Why? Keeping the chamber under the hammer empty isn't an effective a safety trick with modern revolvers having blocks to prevent a negligent discharge - but it means he has an extra half-second or so of thinking time while he consciously cycles the action to bring a live round under the hammer. Gotham is too dangerous to be unarmed - and as a police officer that's not an option - but at the same time a split second of thinking time may prevent a repeat. Harvey is so shaken he's willing to increase the risk to himself to mitigate the risk to others - quite a change from his early characterization.
Gordon's answer to Harvey's "Who is he?" when he and Harvey see Batman for the first time is that he's "A friend." Depending on one's opinion about Jim Gordon realizing who's under the cowl, that comment can be taken very literally.
Babs names her daughter "Barbara Lee Gordon", so the girl will always know who she can count on. There'll be a fourth name added to the list of people whom that child can count upon someday, when she takes up the mantle of "Batgirl": a feminized version of that fourth person's name.
When Jeremiah blows up Wayne Manor, his bombs also demolish Thomas Wayne's hidden room and the end of Jeremiah's tunnel closest to Bruce's home. This probably means that the area surrounding the hidden room was also blown apart, giving Bruce room to expand that smaller hidden office into a larger base of operations that will eventually become the Batcave. This means that the Joker is indirectly responsible for the construction of the Batcave. Since most of his tunnel appeared to be intact even after the explosion, he also most likely gave Batman a quicker, hidden route directly from the Batcave to Gotham, which will make it easier for Batman to do his job, so nice job fixing it, Joker.
At the end of That's Entertainment, when Jeremiah gets sprayed with Jerome's laughing gas, it at first doesn't make sense why he was able to be sprayed directly in the face with it at all, because any sane person would have dropped the box Jerome sent him instinctively the moment a creepy Jack-in-the-box sprung out of it, either because they were startled or because they were actually coulrophobic. However, it makes sense that even before being driven insane, the Joker would be one of the few people in the world who actually likes creepy clowns, so it stands to reason that he would just be puzzled about being sent a present like that, rather than creeped out. Symbolically, Jeremiah gets sprayed by Jerome's laughing gas and turned into the Joker in part because deep down, he's still more like his brother than he will admit, despite the fact that he spent over a decade trying to be as different from him as possible.
In "Masks", Bruce goes to the house of Tom Elliot and we don't see any sign of his parents around. Not instantly scary you say? Well then, think about what what Elliot did in the comics...
In "The Blind Fortune Teller" we find out the Dollmaker is keeping people as spare body parts. Then you realize what he's done to the kids, and since there are no kids around...(!)
That guy who'd gotten his thumb bitten off in "Masks"? Similarly-maimed Sionis employees are probably part of the Dollmaker's customer base, meaning many of those harvested victims gave up body parts for somebody's promotion, not an accidental injury or illness.
In "Red Hood", Alfred's former war buddy Reginald Payne stabs him. It turns out he was hired by the board of Wayne Enterprises to get close to Bruce and Alfred. The question is, how does the board of Wayne Enterprises know so much about the Wayne butler's past, and that they could count on someone like Reggie to do something so horrible to someone he was once friends with?
In "Everyone Has a Cobblepot" we learn just what kind of man the Dollmaker is, and the consequences of those who fail him. This makes how Patti and Doug act all the more creepy, if justified. Patti in particular looked a little Uncanny Valley in the right light. Was her whole face a transplant, courtesy of her boss?
Victor Zsasz is a psycho, with the only man capable of controlling him being Carmine Falcone. By the end of "All Happy Families Are Alike", Falcone has retired, and nobody knows where Zsasz is.
It gets worse: He's henching for Penguin now, and while Falcone would likely have clamped down on some of his more psychotic activities, Penguin is amused by them.
Penguin's step-family are called the Van Dahl's. This name can be easily spoken in another way-Vandals. This is very appropriate for how they vandalize Penguin's short time with their father-also his own, and one of the very few people who have ever given Oswald unconditional love with no expectation of material reward. Yes, this will probably have very unpleasant consequences for them down the road, but it's hard to feel sorry for them when the Penguinkills them.
Oh it gets Horror-ier. The "Vandals", right? In the season introducing such definitely comic-book elements as freeze guns or resurrection? What definitely comic book character do we know who is actually immortal and has "Vandal" in his name? Yeah, Penguin may have some messed-up relatives on his father's side.
The only reason why the GCPD is able to save Gotham from complete devastation at the end of season 3 is because they'd managed to bring Jervis Tetch in alive earlier in the season, thus ensuring his blood would be available for the antidote. What would have become of the city if Gordon, Barnes, or any other cop had shot him instead...?
Remember Martin, the little boy to whom Penguin became a mentor-figure, and whose death he faked to ensure the kid wouldn't be caught up in the crossfire of the next mob war? Now that Zsasz - the only one who knows where Martin is actually hiding - has defected to Sofia and helped her frame Oswald for the boy's murder, what's to stop him from tracking down and killing the boy to ensure his ex-boss can never be exonerated?