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.
There are many, many tear jerkers in Denny O'Neil and Luke Mc Donnel's early 80's run, when Tony Stark falls off the wagon hard. Rarely has a creative team had a superhero descend so deeply into despair.
Iron Man 167. Tony's coming apart at the seams, still vulnerable from Bethany's departure, and facing attacks on all sides from Obadiah Stane's machinations. He's not sleeping and struggling to stay sober. At his lowest point, he goes to his new girlfriend Indries Moomji for comfort..who tells him off in the most brutal fashion possible. Indries was really working for Stane, toying with Tony's heart in order to break it. It works, and Tony takes a long, hard swig from the bottle Obadiah mockingly sent him.
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 World's Most Wanted arc by Matt Fraction has Tony destroying all of his armories and deleting his memories from his brain, in order to keep his secrets and the Superhuman Registration Database out of Norman Osborn's hands. As he's flying across the world, he's losing his cognitive abilities, similar to an Alzheimer's patient. While he's deteriorating, he spends one last night with Pepper, and finally sleeps with her. Pepper tearfully thanks Tony for everything he's done for her, Rhodey, and her late husband Happy Hogan. Tony asks, "Who's Happy". Even knowing he'd get better, this troper was literally in tears.