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The armor gaining sentience and acting violently towards any perceived threat to Tony, a-la Hypervelocity.
This is actually based on the Mask in the Iron Man storyline, where Whiplash's upgrades, a lightning bolt, and Y2K conspire to give the armor sentience and an overprotective and somewhat psychotic nature.
In "Invincible Iron Man: Disassembled," Tony has been working so long he's growing a goatee, which Pepper claims is "gross," and that "facial hair is not his thing." In pretty much every other incarnation, Tony Stark sports facial hair, particularly a distinctive (un-gross) goatee.
Later on in the same episode, Justin Hammer attempts to hire Iron Man as his bodyguard, to which Tony responds that he's "not the bodyguard type." In the comics, Iron Man's cover is generally that he's Tony Stark's personal bodyguard.
Made even funnier when Hammer pilots his own Titanium Man armor and poses as a hired bodyguard.
At the end of the episode, War Machine mentions that it was Dr. Yinsen who made the pacemaker that saved his life.
Captain America is mentioned on a history test in "Ghost In The Machine".
"Armor Wars" as an episode title, not to mention the negator packs.
Within the episode itself, Pepper suggests that Tony take revenge on Stane, "Punisher-style!"
Pepper dating Happy in "Line of Fire" is a reference to the fact that they were married at one point in the comics. Tony and Whitney were likewise an item, even if she wasn't related to Stane.
In "Titanium vs. Iron", Pepper mentions Moon Knight when she badmouths Ghost.
The Masters of Evil are mentioned when Pepper goes over a list of Justin's suspected criminal connections.
Tony calls Titanium Man a Hammeroid.
Fury quips that Stark International and Hammer Multinational are both "shadier than the Yancy Street Gang."
In "The Might Of Doom", one of the suggested applications Doom might want with the Iron Man designs is to make a Doombot.
Doctor Doom mentions Dormammu as an inter-dimensional alien when explaining that their ancestors would call them demons.
In "Enter: Iron Monger", Stane mentions the Savage Land.
The titular armor is also brought down in roughly the same manner: Stane needed outside help to control the armor's functions, which the protagonists sever.
In "All The Best People Are Mad", a shrink ray using Pym particles makes an appearance, though the person who made it never actually got a shot off.
In "Hostile Takeover," Hammer blasts War Machine with a ray that emits "cosmic rays," which will hurt him without harming the armor. To make absolutely sure The Fantastic Four reference is complete, in gloating about all the different ways the rays might mutate and kill him he goes on to describe The Thing, The Invisible Woman, and The Human Torch. Blizzard also spends the opening surfing around the city like Iceman.
"Extremis" has several. There's the titular serum, Fury making a veiled reference to The Avengers, and Tony not being a team player.
More than that - the first SHIELD Agent taken out by Mallen is named Coulson, and the second is named Dugan (as in a reference to Dum Dum Dugan). Later on, when musing about what college he wants to go to Rhodey mentions the joining the Air Force (wherein his backstory lies in the comics), to which in a similar moment to the "I'm not the bodyguard type" moment (or the goatee moment) above Pepper claims doesn't sound like his thing. When thinking of his college ideas, Tony mentions MIT - because Reed Richards teaches there.
Not to mention a frozen Captain Americahanging around on the Helicarrier.
Shout-Out: More than a few, including K-9 from Doctor Who on a shelf in Tony's room.
"All The Best People Are Mad" is pretty much a Saw movie; Pepper even lampshades it. The title is (as pointed out by a character) is a quote from Lewis Carroll.
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