Mind you the 45 acp was tested and designed using live steer (not gelatin or books). Amazingly this testing on heavy boned, 800 pound animals produced the finest fighting handgun catridge ever conceived. I'm in law enforcement and can say that I've never run up against anyone built remotely as sturdy as a frigging @800 lb steer.
If you're referring to the Thompson-LaGarde Tests of 1904, they were horribly unscientific and inconclusive. Also, the best cartridge in the steer test was, in fact, the .30 Luger.
http://www.sightm1911.com/lib/history/background.htm#test
In actuality, both .45 ACP and .357 Magnum are excellent self-defense cartridges and have both been used and proven for many years (the .45 mainly by the military while the .357 Magnum was used extensively by law enforcement).
With regards to overpenetration, 44AMP really summed things up quite nicely. I would only add that overpenetration has been somewhat exaggerated by LE as a way to justify the carrying of politically-incorrect JHP ammunition.
Also, bear in mind that penetration of soft tissue and penetration of harder targets like sheet steel are very different and what works well for one may not work as well for the other. When talking about hard targets, the key is to deliver as much force as possible over the smallest possible surface area. Because of this, small-diameter high velocity cartridges like 7.62x25 Tokarev, .357 magnum, .357 Sig, and 5.7x28 FN will usually give the best results when trying to penetrate hard targets.
When we start looking at softer targets like human tissue, however, things get a bit more complicated. In this area, the cartridge with the lowest momentum-to-energy ratio will typically yield the best penetration. The explanation for this lies in physics. Momentum is the tendency of objects in motion to stay in motion so the projectile with more momentum will have more resistance to being stopped by soft tissue. With regards to energy, Newton's Third Law states that for every action there is an equal and opposing reaction. Because of this, the projectile which strikes with higher kinetic energy will experience more resistance from the target which will in turn retard penetration. Also, if you're using expanding ammunition like JHP or JSP, the higher energy projectiles will deform more and thusly further retard penetration.
In my mind, it's really a moot point. Nearly all premium JHP ammunition in major calibers is designed to consistently meet the FBI penetration standard of 12-16". 12" of penetration could fairly easily mean completely through the upper torso of an adult male if we assume a straight-on frontal shot much less a shot to an extremity like an arm or leg. In my opinion, overpenetration is an issue better addressed by tactics than by choice of caliber. If at all possible, you should try to position yourself in such a way that a shot which overpenetrates would pose the least risk to innocent bystanders should you be forced to fire your handgun. The best bet, in my opinion, is to use premium JHP ammo which penetrates at least 12" in ballistic gelatin, assume that everything will overpenetrate, and plan accordingly.