This line makes me nervous. Only an average of 3.6% of your available CPU cycles are actually used for user processes (mysql, apache etc). OTHO, system, irq, softirq and iowait takes up more than 90% of the time.
This indicates a problem in your disk subsystem. Either your disk system is not capable of handling the load, or you have a RAID5 system where one disk went bad and the missing data must be recalculated every time with the remaining information on the other disks.