I have been having some luck with MySql lately by modifying the my.cnf file as well as doing some basic house cleaning. On the iBlog server, we had installed a plugin called Counterize which keeps blog stats. It created 5 new tables for each blog and crammed it with lots of entries. Since upgrading to WPMU 2.7 we eliminated the plugin and I just got around to dropping those tables. It seems to have helped.
The other thing I did was install a WPMU plugin called PowerTool. This allows me with the click of a button to delete/drop spam comments, blogs, and users. It also will scan blogs that have not been updated in a set amount of days and delete those as well.
All in all, I think we have a handle on the CPU resources iBlog was consuming doing queries and operating the blog platform for our district.