+1 on the dog, the louder and more obnoxious the better. Aways arm yourself and announce the fact, adding that the police are on the way (even if they are not) and that any intruder that approaches will be engaged on the premise that only a person planning harm would continue to advance given that information. If you truly suspect an intruder, do not go looking for them, rather barricade and protect the family from the tactically superior "high ground" as jayrothWA suggests, and wait for the troops to arrive.
On another note, I am surprised no one else has mentioned having a good, high quality tactical light in the same location as any home defense weapon (or on it, for that matter). The brighter the better, 200 lumens or more. no crappy d-cell maglite or plastic Ray-o-vac. Just don't be a target while doing it. Any cop can tell you that blinding an opponent will put you miles ahead in an altercation.
Oh, and this: intruder+known weapon= no quarter or warning necessary. On the ridiculously slim chance that an innocent person has somehow entered my home with a weapon, does not respond to challenges, or comes closer, I could easily live with myself afterwards.
Since the original post involved a safe in the equation, a hard mounted, manual finger combination mini safe that can be actuated in the dark if necessary would work best, IMO.