The Legend of Zelda: Ocarina of Time, with Link and the Poe Collector; the first time he encounters Link he says: "Oh...you are quite an energetic young man. You're brave and handsome, too... Heh heh heh...your name is Link, isn't it? Heh heh heh...don't be surprised. I can read people's minds. If I looked as good as you, I could run a different kind of business...heh heh heh..."
Sheik: It is something that grows over time... a true friendship. A feeling in the heart that becomes even stronger through time...The passion of friendship will soon blossom into a righteous power through it, you'll know which way to go...
The leader of the Gorons, Darunia, calling Link his sworn brother and wanting to give Link a bear hug along with the other male Gorons for his success in helping rid their cavern of an evil monster. He also gives him the Goron Ruby as a symbol of their friendship. Darunia and the other Gorons become big fans of Link for his courage.
Kafei and Link in Majora's Mask has a following, possibly owing to Kafei's curiosity towards Link and his willingness to trust Link.
Link departs Hyrule in Majora's Mask for the purpose of finding a dear friend. He finds himself on another quest to save the world from the moon crashing down. He defeats the evil behind the plot who was possessing Skull Kid in the form of Majora's Mask. Following being saved by Link, Skull Kid decides he likes him and, as he was looking for a friend to begin with, they end up playing together and a tree stump depicts a drawing the two did of them holding hands.
Cremia and Anju are friends, but with Anju getting married to Kafei, going to Clock Town has started to bother Cremia. Who says Kafei is the one she's pining for?
To be fair, the game itself does, as the first assumption when Kafei disappears is that he's cheating on Anju with Cremia, as pretty much everyone on Anju's family knows about Cremia's unrequited crush. That being said, Anju never doubts Cremia, while she does doubt Kafei.
Not to mention when Skull Kid (while being possessed by Majora's Mask) looks to be frisking Link's unconscious body at the beginning when seeing if he has anything he can steal.
In the Oracle of Seasons manga, Ricky the kangaroo was quite gay for Link: gushing over the Chosen Hero, oozing admiration at Link's sword skills, and openly voicing his disappointment at the possibility of him having a female love interest... Ricky having a pouch makes this one questionable.
The Wind Waker has Carlov the sculptor. After you get the color picto box, you can give him pictures and get figurines that give you information on any character, enemy, or boss (always at least one tidbit the rest of the game doesn't tell you.) Well, if you take a picture of figurine enthusiast Manny (the guy who hangs around the gallery) and give it to him, though he's excited about any subject you give him, he'll gush about this one in a way that's very hard to see as platonic. "That golden, freshly brushed hair... That stylish, yet unassuming bod... Why, this is a mighty handsome man! Mercy! My very soul compels me to make a figurine from this picture!" Oh, and the official art of him is holding a figurine. Of who? Yes, Manny. (Carlov gushes even more about the subject's beauty if you take a picture of Carlov himself, though; he seemingly doesn't recognize the picture as himself.)
Twilight Princess: After her life was saved by her (temporary) Heroic Sacrifice, Midna was noticeably a bit too intimate when it came to Princess Zelda...since they didshare a body for quite some time... This seemed to be returned by Zelda, since in the final scene she appears to be even more disappointed than Link that Midna is leaving forever.
The Legend of Zelda: Skyward Sword: Given some of her dialogue/behavior, as well as how fiercely protective and devoted she is toward Zelda, it can make one a little curious as to the exact nature of the relationship between Impa and Hylia before the events of the game.
In Breath of the Wild, Prince Sidon basically becomes Link's biggest fan after he purifies Vah Ruta and saves Zora's Domain from destruction and often exclaims how incredible Link is with extreme enthusiasm. Additionally, there's a male NPC at one of the stables who will comment that Link has extremely beautiful features and is hit on when he's Disguised in Drag as a Gerudo woman or by an Ambiguously Gay male NPC.