The post about the 9mm having a greater tendancy to over penetrate is true and false. Although it has higher velocity than a .40, it also has less mass. A .40 will typically penetrate deeper than a 9mm, but the 9mm depending on shot location can overpenetrate easier. However all the talk about "what is the perfect handgun" for personal protection is hard to answer because there isn't a perfect handgun, lots of opinions and preferences though.
The 9mm vs. .40 vs. .45 debate is misleading. When people start the process of getting handguns for personal protection this is often the most discussed yet least important factor regarding your future safety(which is the whole point right?)
Many departments carry 9mm, many carry .40 The 9mm has better carrying capacity(more ammo), the .40 does have better stopping power. The 9mm may overpenetrate but are you really gonna choose your sidearm on that? How many times will your family be BEHIND a perp in your home.
A more important difference is the size. A 9mm compact like the Glock 19 is easier to conceal compared to a Glock 23(.40)
1.) Choose a handgun that is comfortable to carry and fire. You may feel more "dangerous" with a bigger caliber but if its not completely comfortable to carry, it will more often be found at home/car than on you. I'd rather have a .22 100% of the time than a .357 20% of the time. The perfect hangun is one you will carry everywhere.
2.) The most important variable that will save your life is placement.
Most carriers worry more about caliber and carrying capacity than keeping up on thier skills and putting atleast semi-regular time in at the range. The ability to HIT your target is the most important factor in saving your life. In my opinion a revolver is an excellent gun for personal protection. In high stress situations motor skils diminish. A revolver is much simpler in design and can't stove pipe(casing doesn't fulling extract) or failure to feed/chamber. Its simple point and shoot. I think the .38 for you wife is a GREAT idea.
Semper Fi-God, Country, Corps