These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Captain Robau, who had about five minutes of screentime, has gone down in Trek lore as one of the most badass captains ever.
Gaila is proving very popular. She stars in one scene, is a face in a crowd scene, and that's it. This may have something to do with her being an Orion who presumably has lots of sex, or just the fact that she's another female face.
She also looks kinda like Dizzy Flores from the Starship Troopers film.
Kind of a meta example: Simon Pegg reportedly loved Scotty's companion Keenser so much that he pushed for him to get a bigger role in the franchise than was originally planned. (In the first draft he was a one-shot character who wasn't seen again after Scotty leaves with Kirk, and wasn't even shown to rejoin Starfleet, let alone become part of the Enterprise crew.)
On the commentary, the "cliffs" in Iowa (actually part of a quarry) were caused by the "2011 earthquake". There actually was an earthquake in an unusual part of the United States (the East Coast) in 2011.
A "lightning storm in space" occurs on the day of Kirk's birth. As SF Debris notes, this makes sense considering, "His father is Thor."
Kirk's mother, played by Jennifer Morrison, names him after her father. Her father's name is James, but he's better known as Prince Charming.
So that's where Kirk gets his penchant for getting into trouble and kicking ass from...his parents are Emma Swan and Thor.
Near the end of the film, Nero yells Spock's name as a reference to Wrath of Khan. In Into Darknesss, Spock gets to yells the iconic KHHHAAAAAAANNNNNNNNNN! himself near the end of that film.
Towards the end of the DVD commentary, J. J. Abrams mentions he talked to George Lucas during filming, asking what would make this film better, and Lucas answered more lightsabers. In 2013, Abrams got named director of the Star Wars sequel trilogy.
Ho Yay: Kirk/Spock is the granddaddy of all slash pairings, and the subtext was definitely there in this adaptation. Kirk/Bones too, what with their Vitriolic Best Buds dynamic.
Like You Would Really Do It: Kirk getting chased by a gigantic toothy monster. Kudos to them for giving the monster a face made of Nightmare Fuel, but there couldn't have been a single person in the audience who was the remotest bit worried for Kirk's health. And lo and behold, he doesn't get a scratch that isn't gone by the end of the movie. Quelle surprise.
And, of course, an impressive subversion with the destruction of Vulcan.
Memetic Mutation: "Fire everything!", "I like this ship! It's exciting!", "Wictor wictor...", "SPOOOOOOOOOOOOCK!"
Chekov can do zat. HE CAN DO ZAT HE CAN DO ZAT! MOVE MOVE!
Moral Event Horizon: For Nero: The destruction of the planet Vulcan and most of its 6 billion inhabitants at the hands of the Romulan crew of the Narada avenging the death of their own planet. The death of Spock's mother Amanda as he helplessly reaches out for her just heightens the tragedy. What makes it worse is that he's getting revenge for something that 1) hasn't actually happened in this timeline and 2) wasn't Spock's fault in the first place: future-Spock did nothing to harm Romulus and simply arrived too late to save it, and worse yet, past-Spock has done nothing pertaining to the incident at all. Nero's pretty clearly off the deep end.
Narm: The absurd overuse of Lens Flares, even when there's no apparent source for them.
"Hi, Christopher, I'm Nero." For how awkward it sounds, making it sound like Nero is a customer service representative.
When Nero finds out that Spock foiled his plans and shouted his name. It wasn't so much the shout that was narmy, but the fact that when he shouted it the second time, Nero looked like he had too much Romulan Ale.
Older Than They Think: In one article in preparation for the film's release, Entertainment Weekly addressed hardcore fan outcry about the redesign of the Enterprise's bridge with a "Through the Years" photo comparison of previous bridge sets, pointing out that it's actually been redesigned significantly for previous movies too—it just got more attention in this one, considering the movie's already controversial Reboot status.
Likewise, the controversial Everyone Went to School Together premise of the 2009 film? Per a Starlog magazine from 1988, the idea was being kicked aroud by Nicholas Meyer and Gene Roddenberry as an alternate universe television series.
Tainted by the Preview: The initial two trailers (the first featuring some shots of the Enterprise under construction, and the second being a somewhat random collection of clips from the film capped off by a shot of Spock Prime) were treated with indifference at best, and outright derision at worst by most filmgoers. Averted in the end however, as the third trailer was much improved and credited with creating much of the buzz that made the movie a success.
They Wasted a Perfectly Good Character: As SF Debris points out, the villain described in the novelization/comic versionnote a working stiff who risks charges of treason to help save his world, working with Spock toward the solution only to have the Vulcans slam the door in his face, dooming his race... and then having nothing to live for but revenge is more complex than what Nero was, even sympathetic, and could've actually outdone Khan. He goes on to state that without this, the version of the villain we get is "Some emo with a trident."
Winona Ryder, in particular, became this in the editing room. They cast her as Spock's mother because there was originally supposed to be a brief prologue scene where we would have seen Spock's birth, with a much younger Amanda Grayson celebrating the birth of her son alongside her husband. When that scene was cut, many people in the audience were left wondering why a well-known actress who could easily pass for 30 had been put in unconvincing age-effect makeup in order to play such a small role.
As a Korean-American, John Cho as Sulu also attracted controversy with fans until George Takei, the original Sulu, explained that Sulu is a pan-Asian character, meant to represent all Asian nationalities. Also, the original Sulu was canonically born in San Francisco (which has a sizable and diverse Asian population), and thus there was no basis for assuming that he would be of a single nationality any more than this would be true of a European, Latino or African character. There is a bit Society Marches On in play here, as people only marrying members of their own national/ethnic group is in decline even in the present day real world, and there is no reason to imagine that 300 years from now such a push for ethnic purity would reassert itself, especially when you have Interspecies Romance going on!