Depending on the books you read, these traits are supposed to make a boy romantically protective, brooding and mysterious, or the sexy bad boy just begging to be reformed.
Personally, I go slightly berserk every time I come across that kind of characterization.
Just as Phoebe North would like to see a little more of that typical adolescent behavior injected into the too-often too-good girls of YA, I would like to see a bit more of the good girl behaviors injected into the boys of YA.
Bring me a complicated, original boy who loses his temper and maybe even punches a wall now and then, but also let him care what his parents think of him, and let him be afraid of the consequences for skipping school. Let sex be intimidating, no matter how bad he wants it, or doesn't want it. Let him be a bit of a geek, without slipping into cliched levels of nerd-dom. Give him a dog who means the world to him. Let him make bad decision--epically bad, too stupid to live decisions, and live with the consequences, and apologize for it.
I've read a few boys who fit the bill. Or rather, don't fit it at all. Boys who are complicated and unexpected, and deserve mention.
Joey Crouch from Rotters by Daniel Krauss is trampled on, abused, neglected, devoted, intelligent, a little bit geeky, but takes no flack, especially by the end. Full of secrets, angst, bad choices, risk, redemption, salvation, and temptation--Joey runs the gamut.
Adam from Gayle Forman's If I Stay and Where She Went should by the stereotypical bad boy, but he's not. He's brave and broken, smart and stupid, emotional and unavailable, kind and aloof... Everything you need for a real human being.
St. Clair of Anna and the French Kiss by Stephanie Perkins is another one. Intelligent and funny, he makes bad choices and has to live with them. He has issues with his father, but they don't rule his life, or impair his ability to make connections with others.
Who are some of your favorite, complex, real boys?