Near the end of the film, just as the sun is about to come up. Jedediah and Octavius show up, alive and well. During the chase with Cecil, Larry saw them crash, and he's having a solemn talk with Roosevelt about their deaths. Then they come striding up, looking ten inches tall, and....
Jedediah: You wont get rid of us that easy.
The beginning of Jedediah and Octavius' friendship might also qualify, especially from the viewpoint of the second film.
At the end of the film, the museum has more people coming in then ever before. And it's all thanks to Larry.
The way Larry got the exhibits to make peace with each other and him: he talked to them and made what concessions he could. It was heavily implied that the older guards led by Cecil would just lock up/restrain them as quickly as possible and weren't very nice to them.
Battle of the Smithsonian
The Tuskegee Airmen acknowledging Amelia Earhart's role in aviation history, particularly her similar position to theirs (black people and females, Once Acceptable Targets no more).
"A lot of people didn't think we could fly either. Thanks for clearing the runway, ma'am."
Also when Larry gives the inspirational talk to a depressed Custer about putting the past behind him during the big battle.
When Larry and Amelia Lookalike hook up (or, at least, it is hinted that they do) at the end.