It's like you asked what's the meaning of life.
Self defense ammo is a question no one agrees with, so I'll give you my opinion.
It really depends on the situation.
First...a home intrusion is different than a confrontation on the street.
A thug on the street wants to make short work on his target and not attract attention. It could (not always) take less effort to deflate this situation. Sometimes just seeing your firearm will make him flee. Therefore you can sometimes get by with a smaller caliber, such as a .380, especially if concealment and clothing is an issue.
However, any police officer will tell you, a home intrusion is alot more dangerous. In this case, the intruder knows he's taking a chance and could encounter resistance, especially if he knows the home is occupied. He has made up his mind on what he's going to do, and the risk is acceptable. Often, he's ready to fight and kill if necessary. So you must be prepared to stop him immediately.
So you must drop him quickly and not give him an opportunity to fight back. Otherwise, you and your family could be dead. Therefore, I would use nothing less than a 9mm and would prefer a 40 S&w or .45 ACP for a handgun. And preferably have a a good shotgun handy as my first choice.
Just my opinion. Hope it helps.