I've seen them most commonly used for divination purposes. When you cast the bones, the positions in which they fall, etc can be used to determine the outcome of your question or reading.
I personally use bones and and other such related materials to connect to certain energies or spirits when doing magical/ritual workings. For example, I have a pigeon foot that I use as a rudimentary amulet of protection. I also have a dehydrated seahorse that I use as a focal point when trying to connect to water spirits or elemental energies for healing purposes.
I've also heard of bones used for housing spirits and thoughtforms. For example, I've a relative that uses a deer skull as a housing vessel for a familiar spirit.
If you do a google search, or do some digging here on the site, you may find a few more articles on the subject.