Art Shift: Each universe has its own art style. The Amazing Universe seems like a comic book brought to life, the Noir Universe is grainy like an old film and sort of has a Batman: Arkham Asylum style, the 2099 Universe looks futuristic and Tron-esque, and the Ultimate Universe has the same art style as the Ultimate Spider-Man game.
Badass Boast: It's Spider-Man multiplied by four. It's to be expected.
Kraven has one before each of his boss fights.
Bad Boss: The Goblin qualifies, but that would be ignoring Hammerhead and the Vulture, the first explicitly stating he has no hope in his henchmen, the second threatening to eat them if they fail to kill Spider Man.
Book Ends: The game begins and ends with the Amazing Spider Man.
Breaking the Fourth Wall: "I'm the Hobgoblin! Every Spider-Man needs one!" Then again, the 2099 characters are aware of the Amazing Spider-Man's legacy.
Deadpool is the master of this trope. At first, it can be explained by him running a Show Within a Show, except...
If you pause the game during either battle with Deadpool, he will start complaining to the player for about 10 minutes until he runs out of lines, after which he'll complain about the lack of pause screen dialogue the developers gave him.
When you collect Spider Emblems in his level, he says "Some people think you haven't completed the game until you've got all of them. Just sayin'."
His pseudo-horse-racing commentary when Spidey is racing the first tidal wave is in-universe, with horse names like Sudden Death and Rising Water. The second one, on the other hand, has Sweaty Controller and Gonna Fail This Level.
Bring My Brown Pants: After outrunning the tidal waves in Deadpool's level, Ultimate Spidey remarks that he "just peed his costume a little bit."
Broad Strokes: The universes in this game don't seem to be exactly like the ones seen in the comics, particularly in Deadpool's characterization (the game actually explains this one as Deadpool coming back more insane than ever), the dubious identity of Carnage (at this point in the Ultimate timeline it would most likely be Gwen Stacy), as well as characters who died in the Noir Universe being completely fine. Deadpool even wonders where the game takes place in the Ultimate timeline.
Butt Monkey: Ultimate Spidey. His hazards are Electro (whose powers are his weakness), being fought by a somewhat Genre Savvy nut that just refuses to shut up, and not just Carnage, but Slayer robots designed to destroy parasitic organisms... which includes the suit that he's wearing. Then he has to outrun tsunamis and collapsing heli-carriers. And Mysterio disses him onhis height.
Noir as well. He manages to get himself caught in a trap in each of his levels. Especially notable in the Goblin's where he's blindsided by Norman multiple times throughout the level.
The Cameo: The wall behind Madame Web displays many different iterations of Spider-Man that didn't make it into the game - Amongst them, are Spider-Girl, Spider-Ham, The Black Spider-Girl from Old Man Logan and many Spideys from the various What If... issues Marvel have released over the years.
Canon Foreigner: Noir Hammerhead: the game developers thought he'd be a perfect fit for that universe, given his M.O. is emulating 1920s gangsters such as Al Capone. There was also no Hobgoblin equivalent in the Marvel 2099 universe; there was a character merely called Goblin, but he was an analogue to the Green Goblin (Miguel even tells Hobby that he's fought a Goblin before).
The DS sees Noir versions of Calypso and Boomerang and a 2099 version of Silvermane (though he's also a bit of a subversion as he turns out to be the original, still alive thanks to being a cyborg).
Canon Immigrant: Given the 2099 universe in the game is based on the traditional 2099 universe, the idea of Kron Stone being Scorpion from Timestorm 2009-2099 rather than Venom as in the classic 2099 universe could count as this.
Lampshaded on a loading screen - It's suggested that they're either the same person, or Kron Stone is just a very common name in the year 2099.
Cluster Shock Bomb: In the future, the word shock replaces the f-word (just as it did in the comic).
Co-Dragons: Scorpion and Hobgoblin 2099 for Doctor Octopus 2099.
Combat Tentacles: Ultimate Spidey thanks to the symbiote suit, Doctor Octous 2099, and Carnage.
Comes Great Responsibility: With four different Spideys, one of them was bound to mention it. Ultimate Spidey lays it out for a SHIELD scientist while cleaning up the mess they made.
Composite Character: Ultimate Deadpool seems to work in a little more of his mainstream counterpart's characterization in the game than he does in the comics.
Continuity Nod: Ultimate Deadpool references the time when Ultimate Spider-Man switched minds with Wolverine.
He also makes reference to Ultimate Spidey's relationship with Kitty Pride & the love triangle with Mary Jane. In the final boss fight of the level, he actually asks Spidey where he thinks the game fits into continuity.
Miguel mentions Flipside during Hobgoblin's stage.
Coup de Grâce Cutscene: Subverted at one point in Juggernaut's stage. Spidey even announces that he's gonna deliver the Coup de Grâce, only for Juggernaut to fling him, saying that he "hates French food."
Cross Through: The Spider-Men don't interact with each other until the very end nor do elements of their worlds ever bleed into others' (barring the Wolverine Publicity below) but the four share the same universe-spanning goal of collecting the Tablet fragments, effectively fitting this game as a Cross Through.
Dangerous Phlebotinum Interaction: Juggernaut gets his hands on a fragment of the MacGuffin tablet which increases his already insane physical strength, but it cancels out his own invulnerability meaning Spidey can take him down.
Dangerously Genre Savvy: Deadpool always keeps around extra cameras, and at least once in the stage, went for the unconventional approach and whacked Spider Man over the head, leaving him unconscious. He also keeps around a lot of fire, likely due to the fact that's a big weakness for the black suit.
Hammerhead knows that Noir Spidey's weakness is to be exposed on light. So, what does he do? He fights with a mounted mini-gun and lots and lots of lamps and lights to expose the poor webslinger.
Madame Web as well. Unsurprising considering that she has to communicate with the four Spideys.
And, of course, Deadpool.
Ultimate Spider-Man: "Is this how my enemies feel when I won't stop talking?"
Deus ex Machina: Juggernaut is able to be defeated by Spider-Man because the power of the fragment clashed with his Crimson Gem's abilities.
The Dev Team Thinks of Everything: Attempting to sequence break in the final battle with Mysterio (mainly by going up to him himself) will result in him damaging you.
Difficulty Spike: The DS game gives you a few weak enemies and a faux-boss fight against Mysterio. Your next fight is against Boomerang, who is impervious to all direct damage and can only be injured if you grab his boomerang and hurl it back at him. Granted, it's easy once you know what you're doing, but his speed makes it a very difficult fight.
The villains to a lesser extent. None of the villains in the console versions appear in the DS version except Mysterio, Electro and Vulture. Even then the latter two are alternate universe counterparts.
Excuse Plot: This all powerful tablet that no one has ever heard about breaks. Doing so can break dimensions. It's scattered over four of 'em. Each with a Spider-Man.
Ultimate Spidey's black suit is arbitrarily given to him to "aid in his quest," though everyone knows it's just to make him distinct from Amazing.
And Noir Spidey is given more of the others' powers to make him a little less distinct, because a brutal gun-toting vigilante would definitely clashed with the rest of the game's style.
Fan Boy: Deadpool's mooks are actually a bunch of Deadpool fanboys.
Get Back Here Boss: Several of the stages are more along the lines of one big boss battle, with the bosses running away and spawning mooks for Spider-Man to get in between them once enough damage is done to them.
Gosh Dang It to Heck!: Spidey Noir has some remarkably mild curses for a gritty 30's gun-toting (in the comics, anyway) vigilante.
Humiliation Conga: More like Humiliation Conga Line. The ending credits show an increasingly surreal punishments for each villain, like Sandman stuck in an hourglass, Doc Ock 2099 acting as a mother to her monsters, Carnage posing for pictures, and Goblin back in the circus. Deadpool arguably gets off the easiest; while he's stuck on a Farside Island complete with palm tree, it looks like he's caught a fish and we all know he has the little yellow boxes to keep him company.
Interquel: The Ultimate section takes place before the Gwen Stacy clone was purged of Carnage, but not before it imitated her and was captured.
Ironic Echo: After Amazing Spider-Man tricks Silver Sable into following Juggernaut's tracker halfway across the city.
Spider-Man: Great! Now it's just him and me. Juggernaut:YOU!!! Spider-Man: (nervously) Great! Now it's just him and me.
Irony: The black suit given to Ultimate Spidey is made to aide him in his quest. Then he finds out that his opponents are Electro, an opponent whose powers are established to be the suit's weakness, Deadpool, whose understanding of the world he's in allows him to figure out what to do against the suit, and in Carnage's stage, the slayer robots will attack yhim due to the suit being a symbiotic organism.
Just Between You and Me: Subverted by Doc Ock. "Hmm, I could kill you or I could explain everything and then kill you... Nah, I think I'll just kill you."
Played straight later in the level, though, when Miguel manages to get her to spill the beans on her whole plan simply by acting like he finds the whole thing terribly unimpressive, despite her best efforts to explain how complex and innovative her plan is.
Mood Whiplash: The second Ultimate Spider-Man segment has Spidey fighting against the wisecracking Deadpool. The third segment involves Carnage breaking free of his cointainment, slaughtering several agents, and reanimating their corpses. Spider-Man's also more serious during this chapter (though he still throws out wisecracks, such as referring to Carnage as "a monster made of malevolent spaghetti") and even lets loose a couple swears. Justified, since this is Carnage we're talking about.
Members of the Enforcers are mentioned during Hammerhead's stage (e.g. one of the Mook conversations is about Fancy Dan, and another is about Snake Marston). The Enforcers were Hammerhead's direct subordinates in The Spectacular Spider-Man and the Noir versions worked for Osborn.They are also no strangers to working for Mob bosses.
And Electro is voiced by Thomas Wilson, who voiced Stan Carter on the same show.
Ultimate Deadpool makes a lot of references to his mainstream counterpart.
Also one of Deadpool's fan boys is Deadpool himself, possibly referencing how he likes to talk to himself.
During the final Hobgoblin battle, Hobby says "Welcome to my reality, Spider-Man! Hope you survive the experience!"-a reference to a semi Running Gag on X-Men comic covers when introducing a new character. ("Welcome to the X-Men (character X)! Hope you survive the experience!")
And one of the Ingame-Achievements (the ones needed to unlock new abilities) is called Maximum Carnage.
Deadpool's TV Show "Pain Factor" is a reference to the gauntlet he went through in Suicide Kings.
Ultimate Spider Man sometimes yells out Venom's classic line of "I'm gonna eat your brains!"
The quarry in Sandman's level is owned by Roxxon, the huge and often evil energy company that operates in the Marvel Universe.
Two posters for the freakshow in the carnival level stick out- one has a fat man that bears a striking resemblance to X-Men villain Blob, especially fitting since his origin was him as a sideshow freak, and another advertises a FantasticRubber Man.
While not definite, it's likely the Juggernaut being in the game is a reference to the Roger Stern story "Nothing Can Stop the Juggernaut", from Amazing Spider-Man 229-230. It's well remembered, and one of the very few times Spidey and the Juggernaut have fought. In fact, its climax was at a construction site- the same area where the Juggernaut is faced in SD.
The achievement for beating the Juggernaut even references the title of this story and its more recent follow-up.
New Powers As The Game Demands: To keep the four Spider-Men's abilities consistent, Spider-Man 2099 gets spider-sense, while Spidey Noir gets improved web-shooting abilities; the changes are lampshaded by the characters themselves.
Spider-Man Noir also loses the revolver he used in the comics, probably because it would have been too difficult to balance and would have shifted the Noir segments into Third-Person Shooter territory; after all, the X-Men Legends and Marvel Ultimate Alliance games have characters with guns. (In the comic, he ditches the gun, but he does that after he kills the Vulture, so...)
Rewarding Vandalism: Zig-Zagged: Played straight by Ultimate and 2099 (destroying the surrondings gives them "Spider Essence"), averted in Amazing's Universe, but Lampshaded as if he would play it straight:
Amazing Spider-Man: I'm Spider-man! That's what I do. Break pots!
Rule of Cool: The most likely reason that Ultimate Spider-man uses the symbiote suit. It also distinguishes him from Amazing Spidey. Madame Webb magically keeps it from going bad, while retaining its awesome.
Tempting Fate: Amazing Spider-Man both lampshades this and subsequently suffers from it in almost every cutscene he's in. Most notable in the Juggernaut's level where this trope is brought up at least 3 times, 2 within the first 10 seconds of the intro cutscene.
The Starscream: Hammerhead tries to pull this on Norman after using the power of the tablet. Then along came a Spider...
Thou Shalt Not Kill: The game strongly implies that the player never kills anyone. This is Lampshaded in the tutorial when Spider-Man 2099 throws a Mook off an elevated bridge, only to have Madame Web whisk him to safety via a dimensional portal.
Also, Noir doesn't have his pistol.
To be fair, in the original Spidey Noir comic, Aunt May lectures Spider-Man about shooting the Vulture. Maybe it got to him.
Too Dumb to Live: Electro for continuing the fight with Spider-Man on the dam after seeing that the rain reacted negatively with his powers.
A S.H.I.E.L.D. scientist giving a tablet fragment to Carnage.
Mysterio for making a last ditch attempt to regain the ToOaC in the face of four different iterations of Spider-Man. Lampshaded by Amazing Spider-Man.
Silver Sable follows the tracking device she'd placed on Juggernaut to the other side of New York after Spider-Man threw it away to get rid of her. At no point does she question Juggernaut's sudden departure from the construction yard without leaving a trail of destruction right in front of her, or the speed he was moving.
Very few of the villains in the DS version use their fragment pieces to boost their powers.
Took a Level in Badass: Madame Web for enhancing Amazing's Spider-sense, Noir's webbing, giving 2099 a Spider-sense that slows time, and giving Ultimate the symbiote which she controls with her mind.
And while it's never mentioned, where else would Noir Spider-Man suddenly get the ability to stick to walls?
Totally Radical: Amazing Spidey will sometimes exclaim "Take this, yo!" while fighting.
Ultimate Deadpool would appear to have suffered one since his last appearance in the comics.
Doctor Octopus slowly goes from arrogance to homicidal rage as Spidey 2099 tears her plans apart.
Mysterio in the finale. He goes from what is essentially a god to starting to beg Spidey to stop fighting him, attempting to bargain with him.
Before you rescue any hostages in Goblin's stage, the Goblin spends his time smugly mocking Spider-Man about the hopelessness of his situation. Rescue a few civilians, and Osborn begins to get a mite upset...
What the Hell, Hero?: Spidey gives one to one the SHIELD scientist who thought it was a good idea to give Carnage a piece of the tablet.
Why Don't Ya Just Shoot Him?: In the comics, Noir literally shoots Vulture dead. This isn't the case in-game more than likely due to ratings.
Many were surprised to see that Carnage lived to see the end of his stage. It's the only non-humanoid villain you fight in-game and, considering what it did while it was free, Spidey should have definitely killed it.
This was most likely because he needed to be alive for a later very important story-line in the Ultimate Universe, and the game developers wanted to make things mesh.
Goblin beats the tar out of Noir several times throughout his stage, but never finishes the job. This gives Noir enough time to find out his weak point is his back.
Both Ultimate Spider-Man and Carnage have the ability to create sharp spikes with their symbiotic powers, but neither opts to do so in the punch-out segment.
Wolverine Publicity: Played with. Deadpool is in the Ultimate 'Verse as a villain (though acts more like his Mainstream universe counterpart rather than his evil Ultimate version), but it's not like Spidey needed help marketing the game.
Then there's the fact that you can see Wolverine advertisements in 2099's stages.
In addition to the Hulk (The Amazing version, despite a Hulk already existing in the 2099 universe), Storm, and Black Cat. (This could be another nod to Timestorm 2009-2099, since in that version of 2099 the likenesses of all 2009 heroes were owned by Alchemax and had become their main marketing tool.)