This was essentially another toss-up between Hufflepuff and Gryffindor -- Owen's got the traits of both, and the Sorting Hat would have an extremely difficult time trying to figure out where to place him.
The fact that I personified him as a lion back when we did the animal meme helped. XD
This is a similar situation as the one with Bex. Owen belongs in Gryffindor but doesn't necessarily believe that he does. He's more like Neville Longbottom -- his strength of will is an important trait that I think the Sorting Hat would recognize and want to see fostered. If choosing for himself, Owen would say he belongs with Hufflepuff, but the Sorting Hat knows better -- or at least it knows what Owen needs to recognize in himself. He thinks because of his anxieties and his flaws that he doesn't belong, that because he feels fear that he lacks courage. He's the Cowardly Lion, the one who doesn't think he's strong at all until he discovers that bravery was inside him all along. He needs the reinforcement that just being a Gryffindor would bring him, just to help encourage the traits that make him a successful leader and hero.
The Scarf of Sexual Preference says: I'll Have One Of Everything.