pistol or cigars?

Sorry been away for a bit.
http://www.theboxotruth.com/ is a decent site but look at how his test was conducted, not very scientific.
Personally i am more concerned on how round will act after they have penetrated through a human when i am thinking home defense. Hence just shooting into the boards/drywall is not a good test. He also uses ball ammunition, which i would never recommend for home defense to anyone.

http://ammo.ar15.com/project/Self_De..._FAQ/index.htm
this is a very through and well done test that include the use of ballistic gel, also includes adding layers such as denim and analyzes bullet penetration. Proper selection of .223/5.56 ammunition is a great selection for home defense. This is because these rounds tend to fragment and/or yaw/change direction of travel after hitting the target drastically reducing momentum (mass x velocity). Most 5.56 rounds are already lower mass then pistol calibers, now that the velocity is dramatically especially in regards to it's initial direction the round has less likely to over penetrate.

Over penetration also comes back to one of the fundamental firearms rules. Know your target and what is beyond it. You wouldn't shoot the guy with you child standing behind him, so why would you do it if your child is separated by only a small piece of plaster and paper.

Ultimately the choice for home defense is very personal. You say you are in the service then you are probably familiar with the AR platform and the M9. Go with something similar to them but no matter what you choose practice practice practice with it.