(#) Mongo 2008-07-12
Which House should Harry end up in? That depends on how you think the Sorting Hat decides where each newbie goes.
The "canon" explanation does not work -- why is Percy in Gryffindor instead of in Slytherin, for example -- so I have my own theory for the Houses:
The sortings we know about make sense if the Hat looks at the intensity of three desires: knowledge, recognition/glory and influence/power. Those who have one dominant desire go to that desire's associated House (Ravenclaw for knowledge, Gryffindor for recognition/glory and Slytherin for influence/power) and those with no single dominant desire of the three go to Hufflepuff.
So the question is how do this Harry's desires match up. If your version of him values one of those three things, then he would go in the respective House; otherwise, its Hufflepuff for him.