David Price wrote:
What is best practice for having multiple Wiki's running on one server?
Look at http://www.mediawiki.org/wiki/Manual:Wiki_family. This will give you several options.
Personally, I prefer multiple wikis with each having its own prefix. I also created a "pool" or common wiki to share images and files between the other wikis.
I've used symbolic links to avoid having multiple copies of the MW code.
Consider using shared tables for things like the user tables if it is reasonable to assume that those who register with one wiki are likely to register with the other.
Mike