start off with frame that fits your hand and you're comfortable with. With home defense you don't have to worry about concealabilty so much which makes it easier. After finding a comfortable frame, work with the level of recoil that you're comfortable with; not only managing the recoil but how fast can you bring it back down for a fast second shot (that's also accurate).
9's are decent but lack the high percentage of being able to knock a person down with one shot (mid 50% range), even with the high end shock ammo.
40's improve on this and give very good percentage of knockdown, combined with manageable recoil.
45's rank in the mid 90%'s for 1-shot knock down, have moderate recoil, and due to their low velocity, they don't give you the extraneous penetration (shooting through walls, or through a person's body and hitting an unwanted target). Many police like the 45 but the public perception of the 45 labels it as "aggressive" and opens up more liability issues.
357 mags will give you the best 1-shot knock down (95-98%), rarely will they penetrate through a body, but finding an auto loading 357 mag is hard.
As was noted above, the 10mm is an excellent round giving better knock-down then the 40, and places it between the 45 and 357 on velocity. A side note of the 10mm, it was originally chosen by the FBI as their primary pistol but due to the frame size and recoil, individuals with smaller hands had significant problems bringing it back down for a fast second shot. The cartridge was shortened to reduce recoil, and the 40 S&W was born.
The 44 mag can also be considered for home defense but it's effectiveness is only a bit more then the 40, with additional negatives thrown in. The velocity of the 44 adds unwanted penetration and when used on soft targets (human bodies), the round will often penetrate completely through and through, without expending the majority of the energy in the target. This reduces the effectiveness of the bullet, and adds concerns because the projectile is still traveling and can hit other objects or people.
I've owned and shot all of these calibers and will use them in different situations. For me, I prefer the 10mm or a para ordanance 45.