OK, a few thoughts, may be random at times.
Don't underestimate the deterrent effect of a dog barking. Criminals love soft targets, and dogs don't make it easier on them. On that note think about planting prickly bushes underneath your windows, but not high enough that someone could hide in them. Make sure your outside is well lit, by motion detecting lights and others. On top of the deterrent effect, it allows you to look outside from a dark room without being seen. Reinforce your doors; steel frames and solid locks, not the ones you get at Walmart. You can also easily use X-10 or similar technologies to control all the home lighting from your bedroom which can give you a great advantage.
I have to really disagree with the light shot recommendation. I personally know people who have been shot during hunting season, at relatively short range, with lighter (not buckshot) shot during turkey season. Birdshot is for birds. Use buckshot, I like 00, for home defense. Ballistic gelatin may make small shot look OK, but put a heavy winter coat or leather jacket in its way and the effectiveness is really reduced.
Get a simple, pump, non-tactical shotgun. If you want to put a magazine extender on it for a couple extra shots, OK, but keep the fancy stuff off of it. Find a used 870 for cheap, or a Wingmaster or similar. Mossbergs are OK too, I just like the quality of the Remingtons. 18.5" cylinder bore will do just fine.
Close range shotgunning is more than point-and-shoot. The pattern is relatively small. I wouldn't call it refined aiming, but you're not going to take out everything in a hallway, and yes, you can easily miss someone at 10 feet with a shotgun.
PRACTICE. You don't want to short-stroke a shotgun in the heat of the moment and jam it up. And while we're talking about racking the slide, don't rely on hardened criminals' knees turning to jelly at the sound of the pump. Maybe, but not likely. All you did was notify the perp of your presence. Maybe he'll flee, maybe he'll lie in wait.
Which brings me to another point. If you really think someone is in your house, arm yourself, gather everyone in a room together, like your bedroom, and call 911 from your cell phone (you keep your cell phone next to your bed, right? Phone lines can be cut, even if just to disable alarm systems). Don't go looking for the guy. If you think he's there, defend your family if he comes looking for you but don't go looking for him. House clearing is enough of a pucker factor for several trained police officers, let alone a single, scared homeowner. If he comes to you, you have the advantage.
Don't try to restrain the perp or attempt to cuff him or put yourself anywhere near him. Don't put your foot on his neck. You are placing yourself in a position where he can get to you. Stand back at a safe distance, like you would with a rattlesnake, cover him with your weapon, and call 911. If he gets away, big deal. Your primary concern is to protect your family, not to be the arresting officer.
Forget about non-lethal stuff like beanbags, etc. This isn't the time to mess around with stuff like that. You don't have cuffs, backup, or anything like that. If you need to stop someone, you need to do it NOW.
There has been ongoing debate over the safety of shotgun projectiles versus a light, high velocity fragmenting bullet like the .223/5.56 fired from a rifle like the AR. That's another discussion... but just remember that anything that will penetrate enough to do any kind of damage to a home intruder will blow through drywall like nothing. If it won't, it's not powerful enough to stop a potentially drug-crazed criminal. You don't want it. So always remember what's behind the walls in your line of fire, including your neighbors.
If you're not prepared to kill someone, don't bother with a gun. You don't have to like the idea, I hope you don't, but you have to be willing to do what needs to be done if the situation arises. If not, the gun is worthless at best and could be dangerous to you to say the least. I'm a sensitive guy and I know if I had to take out a criminal who was threatening my family, it would devastate me and affect me emotionally for the rest of my life and I'll always second-guess myself after the fact, but I'll fight to the death to defend my family who relies on me.