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 McDonnel'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 (vol. 1) #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.
Iron Man (vol. 1) #172 has Tony descending even deeper into alcoholism, having given the Iron Man armor to Rhodey so he can drink himself to death without (as much) guilt. Worse yet, Stark International is on the verge of a hostile takeover from Obadiah Stane, and the only thing the staff can do to stop it is get a signature from Tony by the end of the day — who's disappeared to a cheap hotel the Bowery. Rhodey gets Captain America to find Tony and snap him out of his funk, with Steve even swatting the liquor out of Tony's hands. Instead, Tony crawls back to his bottle, saying that if they could feel what he's feeling, they'd know he has to drink. Cap leaves, telling Tony that his father was an alcoholic, and he knows that the only way someone can stop drinking is if they admit they need help... and Tony doesn't even care about his company, his fortune, his friends, or anything else besides drinking himself to death.
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 S.H.I.E.L.D. 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, it can drive a reader to literal tears.
On the topic of him getting better, there's the "Stark Disassembled" arc; specifically, the end of issue #24. After managing to get Tony out of his coma, the heroes are holed up in Sooner Hotel, with it acting as a makeshift hospital... except Tony isn't in his bed. Captain America is discussing this with Dr. Lisk, and Lisk reveals in the brief moment they talked, he might have unintentionally brought up how Cap recently died...
In #22 of the first volume, Janice Cord, Tony Stark's love interest of several years, gets dragged into a three-way battle between Iron Man, Crimson Dynamo and Titanium Man. As she dies her fading last words are "You called me 'darling'... strange... it sounded so much... like the way Tony says it to me...". She never even knew. And the superhero business was definitely not her world. She was practically the definition of an innocent bystander.