Socks and Running.

Triathletes constantly strive to shave seconds off their race time by finding the most efficient way to transition. One method used by some triathletes is to run and bike without socks. Eliminating the time consuming and frequently challenging act of putting on socks can mean the difference between a first and second place finish. The athlete, however, may find the costs do not out-way the benefits. Pain during running and subsequent foot blisters may impede full effort and later training. Lately, however, some manufacturers (1) (2) have developed running shoes with a seamless interior that decrease the chance for blisters.
Interestingly enough, researchers have studied socks and sockless running and have come up with a couple of conclusions:
• "Two different socks were tested, which were identical in every aspect of construction except fiber composition. One test sock was composed of 100% acrylic fibers, and the other test sock was composed of 100% natural cotton fibers. The results showed that acrylic fiber socks were associated with fewer blistering events and smaller blisters (mm2), when compared directly to cotton fiber socks." (Journal of the American Podiatric Medical Association. 80(2):63-71, 1990 Feb. )
• "Despite there being no significant physiological or thermal differences between [standard running socks and ergonomic, asymmetric] socks, the ergonomic sock was perceived to be cooler and was the preferred sock which suggests that subjective perceptions may be more important than objective measurements when selecting a sock for wear during prolonged exercise." (Ergonomics. 47(15):1657-68, 2004 Dec.)
In summary, wearing socks will prevent blisters or limit the foot to smaller blister compared to no sock use (in the traditional running shoe) and ergonomic socks feel better than standard running socks. Science, in this case, backing up common sense.