Here are a couple of standard recommendations for improving DB
performance.
1) A second hard drive for the main database server. You will generally
see a significant performance improvement from having applications,
logs, and the OS on one drive, and only the DB on the other.
2) Make sure the firewalls on the servers are configured not to allow
random IPs to connect to the DB.
3) Move the remaining wiki's off of the DB server, and shut down
everything you can (PHP, Apache, etc).
4) Memory and (to a lesser extent) CPU upgrades can make a significant
impact on performance under the right conditions.
I don't know where the current bottlenecks are, but if it is anywhere in
the DB, the above might help significantly.