There are various scenes in Ocarina of Time concerning Malon that make one double think Nintendo's true intention for Link and his love interest. Here I go through scenes in OoT concerning Link and Malon and even general gameplay to analyze Nintendo's true stand. Just the facts, and observations based on these facts. If you want a compatibility test, check out the Love section of Hero.
1) Fairy Boy. Link's first encounter with Malon ended in him receiving the nickname "Fairy Boy." At this time they're children and it seems innocent enough, but nicknames are often signs of affection. Now, I could get into an entire discussion about how Fairy Boy isn't the greatest name to strengthen a man's ego, but I wont. Because I don't feel like it. Both Zelda and Malon display the same kind of childlike friendship to Link when they're little. They shouldn't be interested in boys yet, anyway. ^_^;
2) Marry Malon? After winning the Cucco-Findin' Game, Talon will ask young Link if he would like to marry Malon. If you answer Yes, he laughs and explains that it was just a joke. "Haw, haw! I was just kidding! Just kidding! I think you're a little young for that, aren't you?" Win the game again and he responds with, "When you grow up, why don't you come to work here, on this ranch?"
3) Knight in Shining Armor. A Gossip Stone near the Temple of Time says that Malon hopes for a Knight in Shining Armor to sweep her off her feet someday. Could this knight be Link?
1) Gameplay. The most basic of elements speaks volumes about the relationship Nintendo carved between Link and Malon. You can beat Ocarina of Time without ever stepping foot inside the ranch. The only time in OoT that you must speak to Malon is in the beginning when Link has to wake up Talon so he can see Zelda. It is not necessary to learn Epona's Song or get Epona. (If you're wondering about the broken bridge in Gerudo Valley, the Hookshot takes care of that.) If Nintendo wanted gamers to think there was something more to Link and Malon's friendship, why make their interaction optional? On the other hand, you must see Zelda at the castle, and at the very end you must save her from Ganondorf. If you don't save Zelda, you don't win the game.
There is no way around Link's meetings with the princess and the princess as Sheik. In Ocarina of Time, Link and Zelda interact the most. If you feel like seeing Malon, that's your choice. In Majora's Mask, Link's only flashback is of Zelda when she gives him the Ocarina of Time and confesses that the "Song of Time" reminds her of their friendship. Malon only appears in the game in the form of Romani and Cremia, her Termina counterparts.
2) Artwork. Malon has but one official picture in which she is standing near Talon and Ingo. Official art shows Link together with Zelda - and no one else. He doesn't even appear with Saria, his best friend. The bond between Link and Zelda is thusly emphasized. Whether intended to be romantic or not, their relationship is an important aspect of the game and was given priority over Link's friendship with Saria and Malon.
3) Manga. The Ocarina of Time manga is licensed by Nintendo and is as official as you're going to get. It's quite obvious in the manga that Link and Zelda develop feelings for each other, though they are never acted upon. The Malon issue is even addressed when Link comes to save her from Ingo, who has taken over the ranch. Link clumsily drops in and asks if she's okay. Malon, tied up on the floor, claims she doesn't know him until he plays "Epona's Song" and her memories of the "Fairy Boy from the forest" return. Link tells her to follow him, but she refuses, saying it is not he who will save her, but her prince. However, after Link daringly saves Malon from a group of Gerudo thieves, she is in awe and wonders if he truly is her knight. Malon is smitten only shortly before Sheik arrives and informs Zelda may be in the desert. Link yells out Zelda's name, causing Malon to get defensive and ask what kind of relationship the hero has with the princess. She gets starry-eyed again, saying, "Alas, how short was Malon's love... I know without asking, from looking in your eyes..."
Apparently Nintendo likes love triangles as much as the rest of us. While the manga is official, it's not exactly canon. Many choose not to believe the added scenes because they were not present in the actual game. Either way, the point is that Nintendo would never license something that conflicted with their original intent.
Nintendo is akin to a teenage girl who has nothing better to do than create drama. There are very strong reasons for dismissing a Link x Malon relationship, but then Nintendo throws in a few curve balls to keep us guessing. However, the hints refusing Malon as Link's love seem to far outweigh those that promote it. Everything can be interpreted except for gameplay, and it is this aspect that is the strongest argument. I have never played a game that made talking to the love interest optional. Zelda is the only one backed by artwork, a manga, and emotion. Link freaks out twice when Zelda's life is on the line. He shows no emotion towards Malon - the player is not even required to save her. She is the only female character that you can let rot. Call me old-fashioned, but I like my heroes to save the ones they love, and I'm going to go ahead and say Nintendo does too.