Hi, I have had a dog which I got from a rescue home. It's a really nice dog but must have been very miss treated as he is quit timid and hangs his head a lot. He has got much better over the last year but he still seems to pee when I give him commands, now its not much but its still not what I want in my house. Is there a way I can stop him from doing this?

Think about exactly what you are doing when you give a command--from the dog's point of view. Are you standing directly over him? Using the stern voice we were all taught in formal obedience class? Are you using hand signals that the dog thinks are a little threatening? Do you use a different type collar when working with the dog than at other times?
Start helping him understand that the exercises are supposed to be fun. I would get down in the floor on the dog's level, and start rewarding with treats if you aren't already. Some dogs can misunderstand petting or praise, but it is hard for them to think a tasty treat is anything but positive. Pretend he is a puppy just learning again. You may find he doesn't understand the commands from this new position right away. Use a clear but pleasant voice to give the command. Reward with a food tidbit and a soft, happy praise voice, and keep excitement to a minimum. You might also look into clicker training, which allows you to work further away from the dog so he doesn't feel so threatened.
Once he gets the hang of this being a game, he should get better and more confident.

As usual, I mostly agree with Carol's answer.

Many dogs eventually outgrow it, but you can reduce it by building the dog's confidence up. Start with obedience training. The key to most behavior problems is approaching things using the dog's natural instincts. Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog. Life is much easier if the 2 legged pack members outrank the 4 legged ones. You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at http://www.dogsbestfriend.com/ As you praise the dog for following your commands, it will build its confidence.

Play tug of war with the dog and lose. However at the end of the game, take the rope or toy and put it up, less the dog becomes confused about who is top dog. Ropes from the pets' store quickly turn to hazardous shreds. Ones I made lasted much better. Go to a hardware or home center that sells rope by the foot. Buy 2' of 3/4" poly rope. Melt the ends, and tie knots in it. Get them as tight as possible, put it in a vise and pound it with a hammer. Watch carefully, and be ready to discard when it comes apart.

Finally, make sure it has a den to live in. If you are not using a crate, buy one. The dog may be happier in its den than loose in the house. It relaxes, it feels safe in its den. It rests, the body slows down reducing the need for water and relieving its self. Dogs that have been crated all along do very well. Many of them will rest in their crates even when the door is open. I think the plastic ones give the dog more of a safe, enclosed den feeling. Metal ones can be put in a corner or covered with something the dog can't pull in and chew. Select a crate just big enough for the full grown dog to stretch out in.

A dog that has not been crated since it was little, may take some work.
Start just putting its toys and treats in the crate. Praise it for going
in. Feed it in the crate. This is also an easy way to maintain order at
Feeding time for more than one dog.

IT'S A SIGN OF SUBMISSION dose the dog also roll on its back when you raise your voice this peeing coupled with rolling on back is the ultimate submission a dog can give (not something you want to achieve by simply talking to the dog) when a dog dose this its say "OMG what have i done don't be upset look i'm vaunrable eat me if you want yourin charge" your dog probably won't stop for a while basically until it knows your not going to eat it or dog anything nasty it may settle down DO NOT SCOLLED THE BEHAVIOUR