In Al Capp's 1934-1977 cartoon series “Li’l Abner” the colorful residents of Dogpatch work diligently to produce illegal moonshine at the Skunk Works. In the 1940's the Lockheed aircraft company’s top secret design, development and production facility was given the same name which they trademarked in 1980. In the 1980's IBM turned to an inhouse skunkworks to figure out the best way to break away from their pure mainframe business model and break into the PC market. And more recently, Motorola's Razr telephone design was completed not at their main R&D facilities but 50 miles away in downtown Chicago.
What makes all these skunkworks similar is that they have all been established outside of typical corporate management constraints. Designers and engineers are given the freedom to innovate and develop ideas that might otherwise not fall within the corporate mold. Usually a skunkworks is a small team with a laissez-faire manager who allows their creativity to reign.
However the original purpose behind the corporate skunkworks was the development of new ideas that would launch radical new technologies like the U2 spy plane. Now a well run skunkworks works closely with marketing, sales and other company departments in order to design new products and services that will help you steal customers from your competition. The old concept of the Young Turks bent on overthrowing all corporate standards fell prey to the cost reduction era of the 1990's. Now, a well run skunkworks will help your business innovate and develop the next generation of products and services.