pezo,
"Best" is a pretty difficult thing to attain, and with ammunition it's likely to be a moving target as companies change their loads and components over time. Not to mention that nasty phrase, "It depends... ." It depends on the gun, the gauge, its weight overall, how well it fits you and other variables. The length of the barrel and its choke matters less than a lot of other things, as long as your defensive plan involves bunkering down in the dark with some light available outside the door of your safe room, and not going out on a single-handed house clearing spree.
You'll need to think about who else is in the house with you and what would happen to your projectiles if you missed your intended target, or if your load penetrated the target through-and-through. How close are the neighbors and what barriers are between you- or can be put between you on the inside or outside- in case something exits your house?
I'd suggest (as a minimum for a 12 ga.) a full house load of 00 buckshot as a basis of comparison. No, not a 3" magnum or even a 2.75" magnum, but a good standard load like Federal Premium (stock #P154 00), 9 hard alloy copper plated 00 pellets at just over 1300 FPS. There are low recoil or reduced recoil loads available from various manufacturers, of course, and some people do better shooting those- but personally I'd rather have a standard velocity load. The reduced recoil comes at the cost of somewhat lower payload velocity and thus potential reduced penetration also.
Yes, there are smaller shot sizes available, and some people prefer them for various reasons. I'm not one who does, I'd rather arrange things so as not to have to worry too much about "overpenetration" and use a load more likely to be effective in turning off the threat. Yes, #4 buck or larger sized birdshot or even light target loads of #8s have been lethal at close range to humans in the past- and no doubt will continue to be. But the chances of an immediate stop are better (though still not 100% by any means) with larger buckshot, because of its increased penetration and therefore increased ability to cause tissue damage.
I'd suggest taking a look at
http://www.firearmstactical.com/briefs7.htm while you are in the process of making up your mind about what defensive load to use. Or if you're really serious, call Paladin and order a copy of the full report, now freshly released to the public for the first time, in time for 20th anniversary of the shootout it covers- see
http://www.paladin-press.com/detail.aspx?ID=1355 . Of course there's no guarantee that whoever kicks in your door at oh-dark-thirty is going to be the equivalent of Michael Platt.
But there's no guarantee he won't be either...
Stay safe,
lpl/nc