Swanfire <3

Rumbelle

Golden Heart and Hooked Queen

This one is pretty obscure, but Sneezy and Happy.
Happy was so protective when Sneezy lost his fairy tale memories at the start of season 2. He looked more alarmed than the other dwarves when it happened, and was really touchy feely with him. In the crowd scene after they announced that everyone would lose their fairy tale memories if they left Storybrooke, Happy has an arm around Sneezy in a sort of hug from behind. When everyone is getting agitated in the crowd in that scene, Happy still keeps Sneezy between his body and arm even when he's waving his arm around.
It's the sort of thing you might not notice if you aren't looking for it, but they do have couple energy then.
When it comes to male couples on OUAT we don't have much to draw on. The way the scenes played out I feel like TPTB intended them to be a couple but also kept them in the background.