Let me confess a weakness--I like boys with girl names.
This is a hard thing as a writer, because boy characters with girl names are not popular in YA. They are confusing at best, readers say, or imply things about the character that you don't want to imply.*
So despite the fact that I know actual non-gay boys named Shannon and Kelly and Lesley and Yancy, it is going to be hard to include non-gay boys with those names in my stories.
The thing that annoys me about this is that girls with boy names are NO PROBLEM, especially if the girl is supposed to be awesome and kickass. Think about it--how many "Sams" and "Alexs" have you seen in books lately? I even saw a "Mike" (short for Michaella) once.
And this prejudice carries over into non-girl names as well. Recently, I had to change a main character's name from Julian (which is TOTALLY a boy's name, Twinsburg!) to Jeremy because the readers were getting confused by his gender.**
The problem, for me, is that a character's name says a lot about him.*** I figure out names for characters very early, and if I have to change one, then I need to find a name that has the same connotations for me, or I will end up inadvertantly changing the whole character. A guy named Zeke is not the same guy as one named Adam. Sorry, but no.
What I do when I'm faced with this dilemma is try to find a name that feels and sounds similar. Zeke/Jake/Mike--these are all conceivably names of the same guy. Likewise Brian/Ben/Brandon (any of which could be an acceptable substitute for Shannon, if you held my hand to the fire) and Julian/Justin/Jeremy.
An alternative strategy is to change the names around the unusual names to make the unusual names stand out more.**** So if I've got a boy Shannon in the book, then I'm not going to have a girl Alex or Sam, and I'm not going to have a male Kelly or Ashley. I don't want to complicate things too much in the reader's mind, so the rest of the characters will be named more traditionally.
A third way is to make the unusual name stand out by giving it a history. For example, in one of my stories, I have a character named Merri, which is short for Meriwether, after the explorer Meriwether Lewis. The very first time we meet this character, he says exactly that, explaining "here's my name, here's what it stands for, and here's how you remember it." (Note that Meriwether Lewis, who the character is named after, is also a boy, which I think helps.) A character with an unusual name that has a history is different from a character with a random unusual name and no explanation.*****
But I'm going to write a book about a boy Shannon someday. Just you wait.
*They mean by this that girl names suggest that the boy characters are gay. Which is only a problem if that's not the suggestion I'm going for.
**We think (meaning the group and I) that part of this confusion may have arisen because (1) they know I'm a girl, and (2) "Julian" is very close to my full name. Incidentally, here's an example of me listening to a criticism because the consequences of not doing so were fairly significant and consequences of doing so were minimal. (How much more minimal could you get that a find/replace? :) )
***Or her, but we're talking about boys, here.
****My books take place in the real world, not in SciFi/Fantasy land, where unusual names are forgiven or even encouraged.
*****Also, a character with an unusual name will probably have siblings with unusual names. It's not common, in my experience, to have a family of Michael, Robert, James, and Llewellyn. Parents just don't typically roll like that without some sort of blow to the head.