When to Scruff a Cat:
For restraint during medical exams, or nail clipping - Scruffing an adult cat should always be combined with supporting the back legs and hindquarters. Scruffing will elicit a calming response when done humanely and by a professional so that medical treatment or exam can be completed.
When safely dealing with an unruly cat - In times of stress, cats want to attack, and then run away. Scruffing is a method to control the head of the cat from biting the handler, while also being able to safely restrain the cat. This should always be coupled with support from an exam table or trained professional for the weighty back end of the cat.
What Not to Do
Scruff an adult cat without support of the back end - Some cats can weigh 10-20 pounds and scruffing a cat of this size and letting her weight hang can cause serious injury to the neck muscles and skin.
Scruff an unruly cat if you are not trained - Leave the wild cat handling to the professionals. If not done correctly, you could suffer a nasty bite and/or injure the cat.