I have built a house in the sky with a Nether Portal in it. When I go into the Nether Portal everything is perfectly fine but when I go back home I don't spawn back in the portal I used to go into the Nether; I spawn in a new Nether Portal somewhere on the ground far from my original portal.

Is the problem that my Nether Portal is in the sky?

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    Yes. If the y level is greater than 128, Nether portals don't really know what to do, since the Nether ceiling is at 128. So it creates another portal (usually as low as possible, often in a cave) – Unionhawk Mar 4 '14 at 23:27