This article is from the Your New Dog FAQ, by Cindy Tittle Moore with numerous contributions by others.
Your new dog may never have been, or actively dislike being, bathed,
groomed, nail-clipped. You will have to proceed slowly and with
patience. Take baby steps. Your dog hates being brushed? Start out
with a warm wet washcloth and rub in short lick-like strokes until the
dog relaxes, then stop. Repeat this and eventually introduce a short
bit of brushing, until the dog relaxes (always end on a positive
note). Eventually the dog will accept being brushed. You can do the
same technique with almost anything else. With clipping nails, first
start with the goal of getting the dog to accept your handling of it's
paws. Then accustom it to having its toes massaged & handled. Then to
having its nails flexed and handled. In the meantime, carry around the
clippers so that the dog learns to ignore them. When you actually
start to clip the nails, clip off a teeny piece off of _one nail_ and
put the clippers away. Later on, do another nail. When the dog accepts
this quietly, do _two_ nails, and so on.
If you find out that your dog is afraid of something, remove it from
its environment, intially. Plan out how you want to deal with it, what
steps and increments you want to take. Then slowly work on it. Work on
one thing at a time to reduce stress on your dog. By doing it this
way, you will build up the dog's self confidence and trust in you.