The best gun for defending yourself inside your house will always be a sawed-off shotgun. You want the shotgun sawed-off to make it compact so it won't impede your mobility too much. Probably should be a semi-auto vs. a pump so you don't have to concentrate on reloading the chamber. Use Buckshot rounds, not rifled slugs. You want to be able to do serious damage but balance that against the possibility that one of your shots will exit your house and penetrate a neighbor's house and cause injury to the innocent (potentially major lawsuit). The shotgun gives a wide spread so you have a better chance of hitting your target, especially if you have just woke from a deep sleep. The flash of the shotgun will briefly illuminate the room/intended target (assumes it is night time) and hopefully guide your next shot.
I've never been a fan of handguns for home defense, especially when you have just waken-up. A shotgun w/buckshot or birdshot has a much greater chance of scoring a hit than a handgun due to the spread pattern of the shotgun.
One problem with getting all worried about the situation and stocking up on weapons and ammo is if you also happen to have kids. You will have to keep everything locked-up so the kids don't get into your weapons and accidentally kill themselves or somebody else. This creates the problem of making your weaponry not rapidly deployable should they be needed in the middle of the night.
Thus, keep a big knife in close reach of your bed as a back-up.
Mr. Spindlelegs