In the episode "Whiplash", Pepper gets Tony to reveal himself as Iron Man to her; the content smile on her face as she nuzzles into his neck is just adorable.
Ivan Vanko's reunion with his family, who after his years of being lost in space, still love and care for him.
During "Pepper, Interrupted" Gene is genuinely worried for Pepper's safety, even willing to draw out Iron Man to get her out of harm's way.
Near the end of "Donít Worry, Be Happy" Whitney poses as Gene in order to get Pepper to safety, course she's doing it to help Iron Man not Pepper. As the pair head for the exit Pepper tells her that they can't leave without knowing if Whitney is okay first. This causes Gene/Whitney to smile in surprise for a moment.
At the end of "Designed Only for Chaos", the Living Laser has a Redemption Equals Death moment, but gets to go out with a smile.
Living Laser: All my life, I was a nobody... then I got those powers, and I used them to hurt you... the one guy who wanted to help me...
Later, after spending the episode coming to terms with the fact that his father at one point designed and manufactured weapons, Tony finally breaks down to Roberta, and she comforts him with reassurances and a Cooldown Hug.
Obadiah Stane may be a major Jerkass to everyone around him, but the end of "Best Served Cold" proves that he truly does love and care about his daughter Whitney.
He goes further at the end of Heavy Mettle in which he makes a Heroic Sacrifice to save Whitney from his own out of control armor.
Pepper giving Tony a ticket to a lecture that they both wanted to see. Pepper just felt that Tony needed to see it rather than her.
At the conclusion of the Makluan invasion, Tony, Rhody, and Pepper's secret identities are revealed to the general public. It takes less than a minute for the rather large gathering of people present to start cheering.