I would write my 2 cents but sean did a great job writing this one up so here it is

The full article can be found here:
http://www.trailslesstraveled.com/viewarticle.php?id=35
Keep in mind that this article was based on a review for Total Chaos' UCA for the Tacoma. So the photos in here will not exactly apply to our 4th gens but it's just a reference point.
Uniball are better because it dramatically increased durability and strength as well as the potential for additional, useable suspension travel with better suspension geometry (on lifted trucks).
This image shows the full extension of the suspension (example but not specifically a 4th gen but this will give you an idea of what kind of angles it experiences). Note the extreme load that is placed on these stock ball-joints. Premature wear is a problem that is accentuated by additional lift, suspension travel and the extra weight of larger tires, not to mention hard off-road use.
The difference in quality is obvious in these two images, and the fault does not lie with Toyota. Ball-joints are adequate for most stock trucks, especially within the range of intended use by the manufacturer. They just werent designed to compete with the race-bred performance of these Total Chaos components.
Once the installation is finished, cycle the suspension fully to check for any interference. Because of the suspension geometry that Total Chaos achieves, on some trucks the spindle will make very slight contact with the upper coil bucket (usually only about 1/16th