As an owner of both of these blades, I humbly submit my interpretation of the diferences between the two. I hope my descriptions are accurate, and I would enjoy a discussion of my viewpoints, especially from those who differ with mine.
These knives are both superb manifestations of expert design in collaboration with a manufacturer known for high standards. The two models represent two very different schools of self-defense with a blade.
The Yojimbo, as designed by Michael Janich, is a weapon built around the idea of disabling your attacker's ability to harm you. This concept is centered around the slashing cut, using the edge of the blade. The knife is meant to be held in a forward grip, with the point upwards from your thumb, and the edge outwards. The design does not preclude using the point, but the edge is the primary focus. An advantage of this design is the short blade, making it legal in more areas. The blade is very much like that on a Stanley utility razor knife. Michael Janich has disseminated a video in which he demonstrates the cruel efficiency of even a stubby razor blade. Due to the compression of flesh upon contact with the blade, the knife can cut much deeper than its actual length, and long, deep cuts are possible. The shape of the handle also allows the knife's use as an impact weapon, utilizing the narrow butt as a punyo. Mr. Janich has long taught a system of engaging an opponent in which a defender might horribly disable an attacker, yet spare his life.
The P'Kal, as designed by South Narc, is meant to be held in a reverse grip, that is with the point downwards and the edge inwards, and to use the point to assault your attacker in a sewing-machine manner, and the edge in a hooking move to shear your attacker's limbs out of the way, thus providing an opening to attack with the point yet again. The technique is ruthless and relentless, with little concern about the survival of your attacker. Another difference with the Yojimbo is the P'Kal's "wave" feature, which allows one to draw a folding knife rapidly, in panic mode, in response to ambush or other unexpected escalation in a confrontation. If we are not allowed to carry a fixed blade in self-defense, a waved folder, with training, gives one a rapid-response capacity. Otherwise, we are left with drawing our folder and utilizing it as an impact weapon prior to opening the blade. See Mercop's description of "folder into the fight" elsewhere in this forum.
Both knives are well built, strong, and reliable. The blades are capable of amazing sharpness. Either can provide self-defense, given proper training and understanding of their designs. We who carry blades with self-defense as one utility should be grateful for Mr. Glesser, Mr. Janich, and South Narc for their collaborations.
I prefer the P'Kal because I have found that, for myself, the learning curve for its utilization is much shorter, and the deployment of the blade is more reliable under extreme duress. This knife, accompanied with one of South Narc's DVDs, and especially if complemented by a training seminar, will give you great comfort as you go down the mean streets.