A Link to the Past
From the moment you enter the light and the Triforce appears, all the way until the credits end. You get music that makes you feel heroic, and as if all your effort had meaning.
The dark world returning to normal, the lives of those you helped. Perfect
ALttP Ending on YouTube
Link's Awakening
The impressive visuals of the much talked about Wind Fish, the notion that by leaving the dream world, means the end of everything and everyone you met. To the glimmer of hope as you find yourself stranded in the middle of the ocean, with nothing in sight.
Link's Awakening Ending on YouTube
Ocarina of Time
Seeing Ganon defeated, and being sealed away (the events only mentioned in ALttP, but never seen)
Whilst not as successful as the ending from ALttP, there is still a nice feeling seeing all the characters you came across living their lives in peace, and that awesome version of Princess Zelda's theme.
Not to mention the minor head-fu_k at the end with Young Link meeting Zelda, and holding the Triforce of Courage
Ocarina of Time's Ending on YouTube
Majora's Mask
One of those times where the ending reflects your level of involvement with the game itself. Depending on how many of the character's lives you became involved with, would determine the ending you get.
Two moments that get to you everytime are Anju and Kaefi's union, and the Deku Butler mourning his lost son.
Majora's Mask Ending on YouTube
Skyward Sword
As much as you may like or loathe Fi. Her farewell and fate will tug at your emotions.
Seeing the whole adventure from Zelda's perspective was a stroke of genius, and then the implications of the final moments. That being the moment that Hyrule was founded, and the arrival of the Triforce for the first time, on the world, and what troubles would arrive from it.
Skyward Sword's Ending on YouTube (its long, but a fitting length after completing the game)
Twilight Princess
Some nice ending shots, and filled with poignant moments. Ganondorf loosing the Triforce's grace. Zant's symbolism of breaking his neck. Ganondorf dieing on his feet. Midna's true form. THE MUSIC. Midna's goodbye, and the final shot of the Triforce symbol above the throne!
Twilight Princess' Ending on YouTube
Killer 7
Absolutely rocking music, and brash end credits. The whole ending sequence to that game was a total mindfu_k which comes from much of Suda 51's work!
One of Killer 7's Endings on YouTube
Ico
Whilst storywise there is not much to wrap up with the end to Ico, and what closure there is feels somewhat unexplained.
DAT MUSIC!!!!!!!
And so sad to see all the environments sinking into the ocean.
Ico's Ending on YouTube
Shadow of the Colossus
More thought provoking, and somewhat sad an Ending, than Ico. But without as an Iconic ending theme. You are left with a cold and haunting feeling when the ending of this game happens...
Shadow of the Colossus' Ending on YouTube
Metroid Prime
Whilst the animation in the background is cool, its the music that makes this credit sequence...
Metroid Prime#s Ending on YouTube
Super Mario 64
It may seem simple, but damn if this ending hasn't stuck with me. The simple peck on the nose, and the music...
Super Mario 64's Ending on YouTube
Mario Kart 64
For the same reason as above, the music!!!
Mario Kart 64's Ending on YouTube
Super Mario World
Not sure about anyone else, but I came away from this game feeling a little sad. I'm sure its the music that did it, but it was nice seeing all the characters getting their curtain call, and seeing them all pass by.
Super Mario World's Ending on YouTube
Mystic Quest
I never enjoy playing RPGs, but I watched my brother play through this one, and I always remember liking the ending to this one. The music as the boat sails off, and the seagull sounds.
Mystic Quest Ending on YouTube
Metal Gear Solid/Twin Snakes - The Best Is Yet To Come
Last but not least...
That song, nothing more to be said...
Twin Snakes Ending on YouTube