I would check into a few things:
What type of platform are you on? Hardware, or virtual? Are you approaching the platform limit in regards to things like throughput or requests per second? If you are using a virtual edition, are there any problems with your hypervisor?
Next, I would switch into bash mode, and use a tool like "top" or "ps" to see which process is using a high amount of CPU time. Top will automatically sort by CPU usage.
What software version are you running? Are you running the latest hotfix? Does the standby unit reflect similar CPU usage or is it idle?