And if you look carefully during the climatic warehouse scene: when Roger and Jessica are tied up, even when they're struggling to not get sprayed by Dip, they don't let go of each other's hands the whole time.
Jessica complimenting Roger on his bravery in the face of Doom and the Toon Patrol, particularly when she calls him her "hero". D'AWWWWW.
When Toon!Doom reactivates the Dip, Roger has Jessica on his lap, getting her away from the Dip. He's ready to put his life on the line if it means his wife gets a little longer to be saved.
The fact that Angelo and the other skeevy barflies didn't end up selling out Roger and Eddie... because Roger made them laugh and brought some happiness into their lives.
This may not seem like much, but maybe the first heartwarming moment was when Eddie met Betty Boop in the Ink and Paint Club as a cigarette girl. He's shocked to see her there on hard times since cartoons went to color. But she keeps an upbeat attitude giving him her trademark 'boop-boop-be-do-boop'. Eddie, the guy who at that point despised any and all toons that he met, actually gave her a genuine smile and remarked, "Yeah, you still got it." Says a lot for the guy that early on.
Also when Betty Boop actually compliments Jessica, a color cartoon, by saying her husband is a lucky guy? And she then cheerfully clicks Eddie's gaping mouth shut.
(Actually, what Betty says in that scene is "What a lucky girl," indicating that Jessica is the one who traded up by marrying Roger. Still quite a compliment.)
This part of the scene where Eddie and Dolores are hiding with Roger in the movie theater gets me every time:
Eddie: You oughta go find yourself a good man.
Dolores: But I already have a good man.
Followed by Roger in full-on Shipper on Deck mode, his ears forming a heart.
The final scene of the film where Porky Pig and Tinkerbell get to close out the film together in their distinctive ways, bringing this unique team-up of animation companies to end in the most charming way possible.
When Eddie, well-established as an alcoholic, decides to take a drink before entering Toon Town, but then visibly toughens his discipline and instead uses the bottle of whiskey as target practice.
He probably was going to use it as target practice anyway, but the heartwarming is that he dumped the whiskey out rather than drinking it.
Herman defending Roger, saying that he doesn't think Roger is a murderer.
The scene where Eddie was looking through old photos of him, Teddy and Delores. The writers even took the time to visually show bits and pieces of Eddie and Teddy's past through other photos and newspapers. It's one of the few times where Eddie actually smiles. This is also considered a bit of a Tear Jerker, seeing Eddie's reaction to the photos with Teddy.
Marvin Acme, sure he was a bit of a jerk spraying disappearing/reappearing ink on Eddie. However he does apologize and assure Eddie, that his jokes are harmless.
Eddie Valiant showing he still has a sense of humor.
Smile, Darn Ya, Smile" always reminds me of how much cartoons mean to me.