There are some obvious ones, some subtle ones...and then the ones we'll get to later, which didn't appear on film at all but were part of the movie's elaborate and expansive viral marketing campaign, including the Daily Bugle that seemed to just never stop cranking out stories loaded with inside jokes for the last six months.
So...what were the ones that stuck out to us while we watched the movie?
The Daily Bugle
After a notable absence from the first film, The Daily Bugle–Peter Parker’s longtime employer in the comics and the Sam Raimi movies–is asserting itself a bit in this movie.
The shot above, taken from the trailer, doesn't exist in the actual movie but literally seconds before, we saw him stop an out-of-control bus with the Bugle logo on the side.
Fun fact, though; that building with the Bugle logo on it is where Red Light Properties creator Dan Goldman has his studio!
A little later, we do get to see the "Spider-Menace" headline teased in one of the Bugle's viral web stories so while we didn't notice much of the physical newspaper, perhaps some of the other stories we've seen online popped up in the film, too, without being noticed!
J. Jonah Jameson doesn't appear in the film itself, but his presence is felt in the movie via e-mails he exchanges with Peter.
During Spider-Man's early encounter with Aleksei Sytsevich, we get a glimpse of his undewear -- and they aren't quite as becoming of a very dangerous man as he might prefer...but they do suggest that he's got a thing for rhinos...!
...Oh, and as we've mentioned before? When he's fully dressed -- but not armored up as Rhino -- Systevich looks a LOT like the track suit "Bros" in Matt Fraction's Hawkeye, who are members of the Russian mob...just like Systevich.
As noted in the comments by diogo02000, Systevich ultimately ends up in The Vault, one of a number of colorfully-named high-security prisons that exist in the Marvel Universe mostly just as a temporary holding cell between supervillain breakouts.
The Oscorp filing system
At one point in the film, we get a little peek at the files Harry has been going through on his dad's computer. Most of the labels are things we’ve seen before–power stations in New York and Oscorp facilities in London, Australia and Oahu.
But then, toward the bottom, there are the files on Dr. Kurt Connors–The Lizard, the first film’s villain–marked as the “Dr. Connors File.”
Beneath that, almost obscured by the video of Electro’s “birth” in the eel tank, is a similar folder titled “Dr. Morbius File.”
In the comics, Morbius is an anti-hero who first appeared as a straight villain in 1971. A scientist whose experiments backfired and transformed him into a vampire, he’s found himself squaring off against Spider-Man, Blade and others over the years. He’s also one of those rare villains that has made a crossover to working as a hero and has found himself the title character in his own stories–or even his own title–pretty often over the course of his existence. Nevertheless, like Deathstroke the Terminator, he always seems to eventually end up on the side of the villains again, whether it’s hunting Blade following the events of Civil War or turning on his former allies when he loses control of his vampiric side.
Seems, almost, like a perfect candidate for a spinoff film in the vein of The Hulk.
In the comics, Morbius is a former Oscorp employee in the comics who becomes a vampire after researching a rare blood disease. This is his second Marvel movie tease but the first one to actually make it all the way to the screen, as he appears in the alternate ending to Blade.
The '60s theme song
You might have noticed that the movie wasn't shy about the theme song from the animated TV series from the '60s. It was Peter Parker's ringtone before he played it on The Tonight Show, which was pretty obvious.
But did you notice that Harry referred to him as doing "whatever a spider can?"
This isn't the first time we've seen the song make its way into live-action cinema; check it out below in Spider-Man 2.
The power grid
The experimental Oscorp power grid (not to be confused with the experimental Stark Industries power grid or the experimental Wayne Enterprises power grid) uses an experimental riff on hydroelectric power, which not only provides an in for the Electro origin story but also seems like it could somehow create Hydro-Man down the line.
Did you notice the guy on the news broadcast (when the reporter was asking for opinions on Spider-Man) with the green and blue striped shirt?
Was that a Sandman nod? It seems unlikely we'll see him again after the abortion of Spider-Man 3. He isn't Venom or anything in terms of being marketable.
Doc Ock and The Vulture
At this point, we know that the movie is setting up Sinister Six and Venom. So none of this is all that surprising, but it's certainly worth mentioning that the wings for The Vulture and Doctor Octopus's harness are seen in the film, coming from the same Oscorp facility that provided The Rhino with his armor.
Of course, this has been much discussed ever since the shot showed up in the trailer, so while it's worth mentioning, we won't dwell on it too much.
In that same computer filing system that mentioned Morbius, we get a storage facility for "Venom." Don't get too too excited, as it's referred to as not being the symbiotic entity that would merge with Eddie Brock, but the actual venom of radioactive spiders which Oscorp is keeping.
Do get excited, though, about the fact that first of all, Venom is coming, one way or another, so this could be it...and if it isn't, it could just as easily be a doorway to Spider-Woman, Miles Morales or some other cool story dealing with another spider-powered hero or villain. Maybe even something in the vein of their upcoming Original Sin tie-in.
The real question is whether it will be Venom Classic or the new version from the comics, Spidey's high school bully Flash Thompson.
In the comics, Gustav Fiers (the mysterious man in the hat) is known as The Gentleman, and he wants to kill Peter in revenge for his parents thwarting his schemes when they were alive. He’s been watching Peter his whole life, waiting for the perfect opportunity to exact revenge. He also knows Spidey's secret identity.
Stan Lee cameo
As we've all known for a while thanks to set photos and interviews with the press, Spider-Man co-creator Stan Lee appears in the audience at Peter and Gwen's graduation.
Lee, of course, is famous for making appearances in nearly every film based on a character he co-created and some he didn't, like the upcoming Guardians of the Galaxy.
Felicia "Black Cat" Hardy and Alistair Smythe, inventor of the Spider-Slayers, appear in brief appearances here, meant mostly to tease the possibility of using them more in future films. Mary Jane Watson once served a similar function, but was cut and will likely now be recast as the actress -- The Fault in Our Stars star Shailene Woodley -- took on the Divergent franchise.
The Raimi films
Yep, there's a wink and a nod to the Sam Raimi Spider-Man trilogy, if Reddit is to be believed. One user noticed this cool little reference:
Did anyone else catch that reference to the Tobey Maguire Spider-man movies? When Peter was searching 'What is Roosevelt?' The computer showed a picture of a gondola with big red letters on its side saying 'Roosevelt'. In the first Tobey Maguire spider-man movie he saves a bunch of kids who were in the same gondola.
The psychiatric hospital that briefly hosts Electro is from the comics, known for holding Spidey’s rogues gallery.
The institute is run by Dr. Kafka, a recast male version of Dr. Ashley Kafka, the founder in the comics. She has been the Doctor to Carnage, Shriek, Carrion, Vermin, Chameleon, Massacre and Venom to name a few.
Well, that’s a cute outfit, Gwen! Where did you get it?
We’ve seen Gwen Stacy in this outfit before, haven’t we?
And no, not just in the paparazzi photos taken during filming. Emma Stone here is wearing the outfit Gwen was wearing in the comics when she died at the hands of Green Goblin.
In the comics, she was hurled from a bridge and died when her neck snapped after Spider-Man tried to save her (this has been debated, but it’s the version I like and I’m writing this, not you).
Sam Raimi’s Spider-Man films bastardized that scene a little bit, with Goblin putting Mary Jane in a similar position, but MJ walked out of it alive. The fact that they staged the scene, though, made it nearly impossible for Marc Webb to faithfully adapt Gwen’s death from the comics. But as you know if you watched, this outfit is more than just a wink and a nod to the source material.