Launchpad going after Laird when he finds out he brainwashed Doofus. Unwise? Quite possibly. But it's a great representation of how much he cares about his "little buddy."
Scrooge and the boys are also more protective of Doofus than normal. The boys order Doofus behind them to protect him from Laird, and Scrooge goes out front with Launchpad to defend them.
The "Rightful Owners" arc:
In issue #4, a dispirited Scrooge gives a brief one.
Launchpad: "...I feel like we let you down."
Scrooge: "Launchpad, you never have and never will let me down."
Also at the end, Donald brings in Camille Leon. The boys go crazy with glee and Daisy greets him with an affectionate "Don!" While Donald tells them to "hold [their] horses" until he can get Camille into custody, he's clearly glad that they're so happy to see him.
At the very end, the triplets and Webby question Scrooge about a statement he made to Rockerduck about "if you want something done right, do it yourself" — didn't they help? Scrooge smiles and gives the following response:
Scrooge: Boys...Webby... yes, even you, Launchpad... you're my family. When I say "myself," you're part of myself. I couldn't have done this without you.
The next-to-last panel shows the party happily engaged in a Group Hug.
At the end of the first comic, Quackwerks is handed over to Scrooge, who puts Launchpad in charge of it, after saying how much he trusts him. This actually highlights a heartwarming Fridge Brilliance in DuckTales as a whole series — Scrooge McDuck constantly gripes about Launchpad's idiocy, crashing habit, and anything else he can think of, but he continually lets him be in a position where he can potentially harm his earnings or his kids — two things we know he cares about. Scrooge wouldn't let Launchpad do those things if he didn't trust him much more than he generally implies.
Scrooge and DD discuss why they bring their kids along on their adventures. While DD states that Gosalyn usually sneaks along despite being told otherwise, Scrooge says that the long term benefits (seeing the world, the lessons learned outside a classroom) are one reason. The truth is that Scrooge can't stand being away from them for too long, and that he doesn't want to drive them away like he did his immediate family in the past.
At the very end of the arc, after spending much of their previous time together snarking at one another, Scrooge and Darkwing Duck give each other a glare after their latest exchange of barbs... and then just smile and shake hands.
Scrooge can encounter Mrs. Beakley in each stage of the adventure, usually in some out-of-the-way location, and she says she's there to make sure he's eating well. (She then provides ice cream and cake, which in the game restore health.) Every time they meet, he gives her a lavish and warmly-spoken compliment, such as saying that she's worth her weight in gold.
In the Himalayas level, Scrooge rescues Bubba Duck, whom he finds frozen in a block of ice. All throughout, Scrooge is talking to the young cave-duck quite fondly, promising to get him back to Duckburg safe and sound.
Also in the Himalayas level, Webby helps Scrooge win the day - not through fighting skills or tenacity, but, in her own words, through kindness and patience.
When he finds the Gizmosuit helmet, Scrooge muses how Fenton seems to get smarter whenever he's in his Gizmoduck persona... and considers that maybe he's a little too hard on his Beleaguered Assistant.
A couple more can be seen at the end of the very finale of the remake:
Scrooge: "That dime's not worth ten cents next to the lives of those boys!"
And just after the final level, Scrooge admits to the boys that while they might've lost the treasures to Magica De Spell's summoning ritual, what he values most of all is that they got to share a big adventure together.
The remake itself was a great big feel in the hearts of fans everywhere, being an amazing expansion of one of the most nostalgic games of the NES.