Moments There are a lot of little moments, especially in the manga, when it looks like the creators intended Link and Zelda to get together.

1. In the game, just after they escape Ganon's Tower, look at the way Link and Zelda look at each other. That glance is one of joy that peace has returned (so they think) but it's also a moment of appreciation for each other.
2. Zelda seems really upset to send Link back to his own time. Link even argues with her: "My own time? Please, wait a second! I didn't come because I was ensnared by the circumstances at hand! Zelda, it was to..." Then he looks kind of sad. It's a really sweet scene.
3. Even though a lot of people pair Link with Malon, there's one scene in the manga that goes against it. As Link comes to save her from Ingo and the Gerudos, Malon is wondering if Link is "her prince." Then they meet Shiek on the rooftop, and Shiek says, "You'd best go to the 'desert of illusions.' I heard a rumor that princess Zelda has been seen there." Link gets very worried-- "Zelda has?!" Malon asks him why he yelled out Zelda's name like that. Then she thinks "Alas, how short was Malon's love. I know without asking, just from looking in your eyes."