Either Majora's Mask or Skyward Sword.
For MM, the ending was amazing. I love how the ending credits showed that everyone Link helped was at peace and resuming their normal lives. For example, it showed Anju and Kafe's wedding, as well as Romani showing her sister how well she can use a bow. I also love how Romani whips her hair back after that. xD That was priceless. After the credits at the end, when Link finds the stump with Skull Kid's drawing, I was really moved. It was like a documentation of their friendship.
For SS, my eyes teared up. It was definitely one of the most beautiful ending ever. Link saying farewell to Fi, as well as saying goodbye to Impa, made me come very close to crying. Aslo, at the end of the credits, when Zelda was finally reunited with her father, and Groose's friends came down to see him, it was really touching. And how Link stayed behind on the surface with Zelda, too. All of it was so touching. It's definitely among my favorite endings in the series.