I use good ol bleach and water and Im a lysol freak.....after cleaning I spray a light mist of lysol on the floor after the floor is dry.
Jimmidy Christmas!........I cant stand ammonia.......it just about kills me to use it..............but very very occasionally I use it because the properties of it are supposed to kill bacterial spores so resilent that bleach doesnt even kill them.
I never use it around the puppies though, I can barely breath with the stuff, I figure my puppies couldnt stand the stuff either.