I've just set up a wiki farm with MediaWiki for the new hippygeek.co.uk. This means running multiple instances of MediaWiki from a single installation, to reduce the amount of work needed to perform upgrades on multiple wikis.
Basically it involves symlinking the entire contents of the mediawiki directory for each instance, with a few exceptions. I'm not sure how well this will scale if I automate creating wikis in this way and I'm yet to attempt an actual upgrade, I'll write about my experiences here.
If you're looking to do this, I basically followed these instructions with a few modifications, like having a separate database and images directory per wiki.
I also set up cleaner URIs for MediaWiki and disabled anonymous editing for now as spam prevention.