Heartwarming: Professor Layton and the Azran Legacy
Emmy and Aurora shopping. Emmy looks so happy to get to do the big sister thing. It's really sweet.
Sycamore contacts Layton's parents, and they show up to see him off before the big trip. Even more heartwarming when you know that Sycamore is Descole, and that HE is Layton's brother... basically, big brother steps in to make sure Layton sees his parents. It's absolutely adorable.
Everything in the ending, often overlapping with Tear Jerker. To list it:
Aurora thinking back to the adventure she had with Layton and the others, which made her realize the humans of the present have already evolved beyond the Azrans as people worthy of inhabiting the planet, even though their technology is millennia less advanced. She then hopes to be reincarnated as a human. Doubles as Tear Jerker because these are her final thoughts before dying with the fall of the Legacy.
Layton telling his biological father Bronev that the only name he needs is "Hershel Layton" and that he considers Roland and Lucille his true parents. As Bronev is taken away, Layton states he hopes to meet him again someday, not as father and son, but as fellow archaeologists and friends.
Descole fakes his death during the fall of the Legacy and is instead rescued by Raymond. He is now free from the burden of the Azrans that had consumed his entire life, and the police won't come after him because they believe him dead. As he and Raymond fly away on the Bostonius, the latter tells his master that he can finally find a new purpose and that he'll be there with him until the very end. Descole smiles and heads towards new adventures.
Definitely also overlapping with Tear Jerker, Emmy prepares to leave Professor Layton's office after her betrayal, reasoning that now that Bronev's Targent is no more, her mission to keep tabs on Layton is finished. Layton argues that regardless of her mission, a professor always needs an assistant, but Emmy feels to be unworthy to continue being his assistant and tells him that Luke is the best person for the role. Emmy starts walking away, but her stiff upper lip finally falters, she turns back and runs to embrace the professor while giving him her goodbyes in tears. Layton puts his hands on her shoulders and thanks her for the three years together.
More moments in the pictures during the credits roll: Grosky gets a promotion for his work in bringing down Targent and catching Bronev, a parallel is drawn between Bronev teaching archaeology to his inmates in prison and Layton teaching it to his students at university, Luke notices a woman who looks just like Aurora walking by and carrying a little baby girl, and Emmy embarks on a new journey by herself. And finally, Layton receives a certain letter, and the opening from Curious Village plays, tying the two trilogies together beautifully.
Everything to do with the Popoņo and the Harmony Ring.
Old Red. Just... Old Red.
By the end of his plotline, the townsfolk that were once afraid of him readily accept him.
Descole's gentle praise of Luke when the boy solves the floor puzzle in the Chamber of Water. Also, the fact that Descole takes a bullet for Luke. Just minutes earlier, Luke was being bratty towards him, but still he saw fit to protect the boy anyway. That made this troper cry.
One of the earlier requests in the dress-up minigame is from Luke's mom, Brenda. Though the finished product looks a tad ridiculous (even Luke admits it's a bit much), Brenda absolutely loves it, and so does her husband Clark.
It's revealed in this game that Grosky and Chelmey are actually brothers-in-law, and you get to see Chelmey and his new wife Amelie around the world in their honeymoon!
In the ending credits, Luke sees a woman pushing a baby carriage, the woman looks somewhat like Aurora, implying the baby may in fact be, the reincarnation Aurora wished for. It was never stated when this scene takes place, but if it's around a year later. That would fit in perfectly