Let's start with the basics. Manure is always contaminated. The bacteria of the body is disposed of this way, some are alien to it, and some are friendly that works well in one area of the body, but only that area. E. coli is one of those. In Europe the authorities are monitoring communal bathing places and any trace of E. coli will shut the entire beach, since E. coli are causing infections when it turns up in places in the body where it shouldn't be - which happens if you're accidentally swallowing the bathing water.
To kill of the germs it's common to compost the material. The easiest way is to heat compost (or whatever the term is in english, my dictionary is failing me on this one) the manure for a few months. During that time the temperature is rising to about 60¤C (140¤F) (or above) which kills most dangerous microbes. To be on the safe side you can then put it in an ordinary compost for some months - in that case the entire process takes about a year.
Contaminations or not, manure is a popular and wellspread fertilizer. Fact is there are lots of different kinds to use, all with slightly different features due to their source. Most of them do not contain as much nourishment as urin, but have the advantage of adding soil material to the ground.
Farmyard manure (horse, cow, pig, sheep)
Can be used fresh, but keep edible vegetable parts away from it (horses, cows, pigs and sheep carry E. coli too). Normally you use single composted (in Sweden we say that the manure is "burnt" - apparently my dictionary was written by a citydweller, he doesn't know the correct english word for this one) or doubble composted manure since it smells less. Fresh manure, on the other hand, is good to use if you want to make an outdoor hot bed, and on the hole I think farmpoop is best used outdoors - where it's great! Indoor gardeners may have less use for the product.
If you want cheap farmyard manure you can call in on your local stables and see if they want to get rid of some. In Sweden stables are more than happy to give it away since this solves a garbageproblem. You may need to pick litter out of the mound you get, but otherwise the quality is alright.
Contains a lot of nitrogen and may need something rich in potassium as a complement, ash for exemple. Decomposes fast and is used if you want to "overfeed" some plants or give the garden a quick meal. You can buy this one in pellet form and advanced indoor gardeners who makes their own soil may have some for special plants.
Kitten manure WARNING TOXOPLASMOSIS
If you've been adopted by a cat it may be tempting to pick the poop out of the litterbox and use it as fertilizer. Don't do that. Cats are the major host for a parasite called Toxoplasma gondii which may cause spontaneous abortions, adult eye injuries in surviving fetuses and infected adults may get encephalities if the immune defence is weak. The infection may be dormant, but if it breaks out you need expert medical care, there are no easy medication. (Wild animals can contract the disease too. Otters, for exemple, gets something that looks like a perpetual epileptic attac. In this case the parasite has entered the water they live in via badly constructed toilet sewers where people dump their kitty litter.)
Again: don't use kitten manure, and don't put it in you compost.
Yes, you can use your own products, but be extra careful in redusing contagiums. When using animal manure you have the advantage that not all illnesses carried by the beasts are compatible with humans. In human manure they are. Many county authorities in Sweden ask for double composting of the end product before they admit anyone to install a composting toilet for that reason.
Is it difficult?
I've spent quite a lot of time discussing contagiums and different kinds of composts. This may make it seem like using manure is an overly difficult process demanding protective clothes similar to those used in nuclear power plants. The fact is that handling manure is easy, you only need space and patience. I have a few friends with a composting toilet, when the compartment is full they exchange it for an empty one. The full one is taken outside, a small amount of soil is poured into the bucket and then they put on (and fasten) a lid. During half a year the container is left on its own while the microlife of the soil does its work. That's easy, isn't it? If you want to double compost the products you can pour them into a normal compost when the six months are up (if you have a small one I suspect you should mix the manure with other stuff) and leave it to mature.
Farmyard manure is best handled by putting in a big heap untill the burning phase (the single composting phase) is over. If you are buying from a farmer it's possible that she or he already have done that for you.
This is the ideal natural fertilizer for the indoor gardener. Odour less and surprisingly devoid of contagiums, and in addition it's easy to keep the producing 'beasts' at home. The product smells like earth and keeps moist well. A vermicompost gives you the right amount of fertilizer for your indoor gardens, while it can be hard to make it stretch over your outdoor beds. This is my first choice for small scale and indoor farming - get a vermicompost ;)