This spring when you turn under your cover crop and spread fertilizer, think twice before using manure--Not all manure is created equal! Don't get me wrong, manure is high in organic matter which is good for building and maintaining soil tilth. But in terms of fertilizer, there are a lot of variables.
For instance, horse manure is often full of weed seeds, can be high in magnesium (over time causing a toxic buildup in the soil) and lower in nitrogen than chicken manure. Ann Lovejoy, a well known Pacific Northwest Gardener won't use it at all. Here's why:
Since a lot of nitrogen is in urine, chicken manure is higher than many other manures because unlike mammals, they have one waste product coming from one place (the cloaca). If animals are kept on bedding however, the urine is caught there and it should be used with manure to create compost. One caveat exists of course-- the carbon to nitrogen ratio of the bedding may be so high, you actually have to add more nitrogen for effective composting.
Some other animal manures that work great are rabbit, goat, and dairy cow. It is always best to get manure from organically-raised animals. This is because some plant pesticides are persistent even after passing through the gut of an animal. Also find out if the manure is from animals that received any antibiotics or other drugs. One horse farmer I know separates the manure based on de-worming time.
If you get fresh manure, it's best to acquire it in the late winter, so it doesn't smell as bad, and start composting it. It needs to be composted so that the nutrients are available to your plants when they start growing. Also, fresh manure can have pathogens and parasites, so don't use it fresh on the garden. Pre-composted manure is available at many nurseries, but it is pricier than the fresh.
For more in-depth information, check out these websites: