A few in the infamous Demon in a Bottle story, such as Tony desperately admitting to Bethany that he needs help.
Not to mention Tony's armor malfunctioning due to sabotage and killing the foreign ambassador, who, up to that point, was Squeeing over the chance to actually meet his hero, Iron Man.
Tony and Pepper when having to make the decision to unplug Happy's life support after he falls into a vegetative coma fighting off Spymaster.
Maria Hill's backstory, as revealed in Invincible Iron Man. Her mother died either during or shortly after her birth, her father hated her for it, and she grew up with everyone telling her that she was terrible, from her childhood, to being kicked out of high school, to when she was in the Marines, to when Fury was yelling at her. On top of this, she's shown being treated badly by the SHIELD agents around her, with one saying "so long, sweet cheeks" and her narration says that she can't resist slapping back once more. Is it any surprise that Maria's first instinct is usually to attack people?
Even worse—we see a photograph of Maria's desk when she's clearing it out - it's of her shaking Fury's hand. This implies that she used to look up to Fury, but in another issue where he broke into the Helicarrier to warn her about the Skrulls, he didn't even remember meeting her before.
The opening scene can really hit home for people who have had to take care of their dying parent and that itself is another tearjerker.
Subtle Bilingual Bonus with Ivan at the start of the scene. Anton calls his name a few times. Ivan ignores him. Anton uses Ivan's diminutive name (the one more associated with his youth), Vanya. Ivan pays attention.
A fridge tear jerker from 2 when Tony is in his suit, munching on a donut, sitting in a giant donut, wearing shades. Although this scene is played for laughs, when you subtract the amusing background music used in the scene and the inherently funny nature of Iron Man sitting in a donut, this is a really depressing scene. He had just gotten into a fight with Rhodey, whose response was to take his Mark II suit to the Air Force, trashing both their friendship and Tony's desire to keep his tech private. His palladium poisoning was getting critical, leaving him with mere days to live (less than 72 hours, according to the tie-in comics), especially if he kept on accelerating it by using his armor. And after an attempted night of over-the-top partying was crashed by his best friend, Tony was so desperate to spend the last days of his life enjoying himself in new ways that he was reduced to sitting there on top of a donut store while wearing his armor, and eating some donuts. Good thing Nick Fury showed up.
The fight between Rhodey and Tony. It's pretty badass at first, but then they start talking to each other. Take it from each end. Rhodey is desperately trying to save his friend from self-destruction, while Tony is coping (terribly) with the certainty of his death.
Tear Jerkers for the Marvel Anime: Iron Man:
Tony discovering Yinsen is alive, but has gone completely insane.
It makes Yinsen's second death all the more heartwrenching.