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.
After getting rescued by Eddie and untied by him, Jessica rushes to Roger, kisses him over and over again and calls him a pillar of strength. It's so cute.
"Roger, I love you. I love you more than any woman's ever loved a rabbit." Admittedly, it's a bit of an Overly Narrow Superlative, but the sentiment's still very sweet.
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.
After Eddie saves Roger's life the second time by tricking him into taking a drink (and firing a Chekhov's Gun in the process), Roger commends Eddie on his quick thinking.
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, and Betty explains that works been a bit slow for her since technicolor cartoons have become the norm. But being who she is, Betty 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 gives her a genuine smile and remarked, "Yeah, you still got it." Says a lot for the guy that early on.
It's easy to miss, but Eddy has a Betty Boop toy in his office (and the only piece of 'toon Merchandise on his desk), which imples that she is a cartoon that he fondly remembers from his childhood and that he still values their friendship.
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 even forming a heart.
Roger: Pb-b-b-blease! Don't mind me..!
Even before Delores shows up, after Roger asks Eddie straight-up about what happened to him that led to his hatred of Toons, Eddie decides to come clean and reveals what happened to his brother, Teddy. This is heartwarming for two reasons:
1.) Despite how he's treated Roger up to that point in the movie, Eddie (at least one some level) seems to feel comfortable enough around Roger to tell him something extremely personal (and something that's implied to have happened relatively recently).
2.) Roger's got nothing but sympathy for what Eddie's had to go through since his brother died—Roger's also horrified that it was a Toon that killed Teddy, especially since (as previously mentioned at earlier points in the movie) Toons are meant to be funny and make people laugh and feel happy.
And before that, they were watching a Goofy short, where Roger is in hysterics and hails Goofy as a comedic genius. When you remember that in this universe they are actors working for rival studios, it is heartwarming to see such praise from one artist to another. It's even more relevant since—if the comments of the other characters can be believed—Roger is considered to be a superstar and thus at least equal to Goofy in-universe, if not above him.
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.
This was Mel Blanc's second-to-last performance before his death the following year. He not only gets the last line of the movie, but also got to close out his career with one of his most famous characters saying, arguably, his most famous catch phrase.
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 part is that he dumped the whiskey out rather than drinking it.
Eddie decides to turn over a new leaf, give up the booze, and do something worthwhile. And why does this toon-hating detective decide to do these things? To save his friend—WHO'S A TOON.
As a Freeze-Frame Bonus, a little engraving on the case of the 'Toon gun reveals Eddie received it from Yosemite Sam, who had given it to Eddie as a thank-you-present for some favor Eddie had done for him in the past.
Speaking of the gun, when Eddie opens the lid for the bullets, they are mentioning how they haven't seen him in five years. Are they angry that he's ignored them all this time? Nope! On the contrary, they are overjoyed to see him again and when he opens his gun, they readily jump in with an excited yell.
Herman defending Roger, saying that he doesn't think Roger's a murderer. What really makes this touching is that Herman simply can't stand Roger sometimes, what with the latter frequently screwing up their scenes together during filming.
Eddie flipping through the photos of him and Deloris on vacation. It's one of the few times Eddie actually smiles. Then he gets to the photos of Teddy and we're treated to a pan-over of photographs and newspaper clippings that tell the story of how much the two brothers loved one another.
Marvin Acme may be a bit of a Man Child, but like his buddy Roger, all he wants to do is make people laugh. He sprays in disappearing/reappearing ink on Eddie, but is quick to apologize when he sees Eddie doesn't find it funny. Even his will refers to the Toons as "those lovable rascals!"
Eddie Valiant showing he still has a sense of humor.
If there were ever a song to describe how great cartoons are, it'd be "Smile, Darn Ya, Smile."
It's brief, but there's a scene where Eddie gets onto the back of a streetcar and two kids are trying to do the same. Without hesitating, he gladly helps them up onto the back of the streetcar with him.