Well, I really like 'A Different Destiny' in the Zelda and Ganondorf fanfiction world. It presents a scenario where Ganondorf and Zelda have to team up against a greater evil. This completely flips the traditional view of their relationship. Then there's 'The Truce' which shows how a temporary peace between them could lead to a whole new world of possibilities for Hyrule. Also, 'Ganondorf's Hidden Past' reveals some backstory that makes you see him in a different light.
One great 'Zelda and Ganondorf Fanfiction' is 'The Battle Beyond Time'. It delves deep into their eternal struggle, showing a more complex relationship between them. Another is 'Ganondorf's Redemption Arc' which takes an interesting turn by exploring Ganondorf's possible change of heart. And 'Zelda's Understanding' is also good as it focuses on Zelda trying to understand Ganondorf's motives rather than just seeing him as a pure villain.