Irish and Scots Gaelic have the word "rún/rùn" (the former being Irish, the latter being Scottish) and it also means "secret" and is often used as a term of affection: "mo rùn geal, dìleas" ("my faithful, fair one").
If it was me, I wouldn't give my child the first name Rune, as it's a recognizable English word. I'd definitely consider it as a middle name, though! I really like it.
When I first came across this name, I thought it was unpleasant and too much of a fantasy name. But I love the sound of the name; from what I've seen of pronunciations, this name sounds very good. I can't see naming a child this, but it has an almost dreamy quality. Strange.
In very few of my stories, there is a mysterious character by the name of Rune. She is female, though, not male. Usually she has a confusing past that leads to her adopting her nickname as her given name--and she got the nickname Rune because of all the strange tattoos covering her back. It ties into the story nicely, as she isn't just plopped in there as a "oh, that's cool, huh?" element.
I really like Rune with either pronunciation. I do however like it better on a girl. I think there is a sort of charm behind the name that would be cute on a girl where as on a boy it's not quiet masculine enough. Great alternative for girls Rain, Rose, Renee etc.
This is an adorable name for a boy. I can also see this as a character name in a fantasy or sci-fi tale. I like how it is short and sweet, but it also strikes me as a powerful name.