SKUNKS
Although the solution for pet urine below can help with skunks, the most efficient I have found are speciality products from a Québec company SOS ODEURS. They have shampoos for your rugs and the fur of your pets, but they also have spray on solutions for the hard surfaces and landscaping around your house, their MH-45 solution. I have used this twice with amazingly good results. If the odour is in your ventilation system, spray some of this into the system from the same intake that pulled in the skunk smell in the first place, with your system runing. That should chase down the odour and even neutralize your fileters.
URINE
Many odours can be eliminated by soaking the troublesome area with baking soda. One of the tricks to make the baking soda the most effective, such as to remove pet urine from a rug, is to add water to the baking soda to make a paste. Work the paste into the fibres of the rug.
Then cover it all with plastic wrap to prevent it from drying out quickly. Leave it about a day, remove the plastic, remove most of the soda and let it dry. Then vacuum it up. A treatment or two will often remove both stains and odours.
Even more effective than the good old baking soda for removing odours are cleaners with enzymes in them, often sold at pet stores. The enzymes are actually small bacteria that eat the organic material causing the odours.