Well, I've fixed the problem. Some corrupted db tables were causing MySQL to use all available CPU. Yesterday, I set up eAccelerator (works great!) and also Donncha's site-wide-tags. I also tried wp-super-cache and thought there was a conflict with eAccelerator but was wrong about that. They are working well together now. The fastest the site has ever been.
Around the time it started going wrong, lots of these messages appeared.
PHP Warning: mysql_connect() [function.mysql-connect]: Lost connection to MySQL server at 'reading authorization packet', system error: 104 in /var/www/html/chat/bb-includes/backpress/class.bpdb.php on line 123
and:
[Mon Oct 13 16:56:41 2008] [error] [client 194.80.61.106] PHP Warning: mysql_connect() [function.mysql-connect]: Too ma
ny connections in /var/www/html/chat/bb-includes/backpress/class.bpdb.php on line 123
This is a bbpress error (also on the same server) and a couple of days ago, I linked WPMU to BBPress 1.0a using Sam's bbpress-live plugin. However, bbpress has no users so I'm not sure why it suddenly went out of control.
That's all I can tell you. It's made me get around to doing a few server chores that I've been meaning to do for a while.