adding a ticket in 1.9.4rc2. timed max 5 seconds.
Debian wheezy 7.6
model name : Intel(R) Xeon(R) CPU X3470 @ 2.93GHz
Ram 8Gb, ( 5 websites. 2 average use, 1 heavy. )
run mysqltunner to optimize you mysql settings. ( or mysqlprime.pl ) google for it.
and run hdparm -tT /dev/sd?? check iotop. i think you hdd io is slow. set swappines to 10 or 20 to use more ram for caching before swapping.