The two wikis I set up for other groups to manage their documentation have now expanded to four (including my Medical Physics wiki). At about 45 MB for just the code, I realized having multiple Mediawiki installs running around was quickly going to suck up a lot of disk space and be a PITA to manage, especially for upgrades.
After trying it out on my test server, I now have all four wikis running off the same installation (took about 20 minutes). One copy is much easier to maintain than 4 separate ones, although one significant flaw in Rumberg's approach is that if future versions introduce new files, some of them (depending on where they're located) will have to be manually linked into the other wiki's. Still much better than having to manage multiple installations.
Now what I need to do is set them up with a common help that's sufficiently customized for the local installation.