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, who in response had taken 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, with possibly mere days for him 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 message Howard Stark left for Tony at the end of the Stark Expo film.
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.