I'm almost at a close with this problem. It appears that Apache is under a DoS attack to the one site that is using all the resources. I recompiled Apache and included mod_dosevasive.
http://www.nuclearelephant.com/projects/dosevasive/
It seems to be running ok but it runs best with KeepAlive set to off. I need to tweak the configuration for mod_dosevasive. Looking at top, the resource usage is respectable but it's still somewhat high. An average of 69.4% idle, normally, it is 99.4% idle. Overall, that's better than 0.0% idle.
I thought brute force hacking was bad. I would welcome that compared to this.