A lot of the things you can put in a dog kennel to improve the smell -- such as garden lime and soda ash -- are somewhat caustic, meaning the chemicals can burn your dog's feet, cause skin problems or make them sick. You can mix up your own kennel freshener, but be aware that even the more benign things you can use to cut odors can negatively affect your pet if used incorrectly.
Scoop up and dispose of all the dog's waste matter. Rinse the kennel with cold water from a hose, scrubbing any deeply stained areas with an old broom. Pour a 50/50 mix of antiseptic mouthwash and water in a spray bottle. Shake the bottle to mix the ingredients completely, then saturate the kennel with a heavy mist of the spray. Allow the spray to dry completely before your dog returns to the kennel.
For really strong-smelling dog pens, try a bleach-based spray to cut the odor. Bleach will add a different strong smell, but will cut the urine odor. Clean the kennel normally, then mix up the spray. Pour 1/2 cup bleach in a 1 quart spray bottle, then add 2 cups tap water. Squirt a heavy coat of the bleach odor remover all over the kennel, then let it dry completely before using the kennel.