http://iroi.seu.edu.cn/books/ee_dic/whatis/skunkworks.htm
A skunkworks is a group of people who, in order to achieve unusual
results, work on a project in a way that is outside the usual
rules. A skunkworks is often a small team that assumes or is given
responsibility for developing something in a short time with
minimal management constraints. Typically, a skunkworks has a small
number of members in order to reduce communications overhead. A
skunkworks is sometimes used to spearhead a product design that
thereafter will be developed according to the usual process. A
skunkworks project may be secret.
As for the term's origin, we like what Harry Newton says in
Newton's Telecom Dictionary:
"Term for usually-secret high-pressure/high-tech research group in
a company or government, often populated by people who don't see
much sunlight or soap. Hence the name, skunkworks."
The name of the animal itself was derived by early American
settlers from the Algonquin Indian seganku.