You are monitoring the SMART values of your disks right? They're usually a real good indicator of the health of the drive.
Thought I'd check out the SMART value of the disks in my desktop today (while checking if I had notifications from smartd on).
Low and behold, the Load_Cycle_Count (LLC) was really high, much higher than power_cycle_count on the 3TB WD disk I have. It turns out this is quite an old problem so there are a few posts about this on the Internets. The Interwebs says max in the specs are 300k load cycles. Smartctl -a says I'm already at 218602 after 9302 power on hours (387 days but I power off the computer at night).
Disk:
Model Family: Western Digital Caviar Green (AF, SATA 6Gb/s) Device Model: WDC WD30EZRX-00DC0B0
For Windows there's a wdidle3.exe that is a DOS program that one can put on a bootable floppy (...) and boot a computer on to change some stuff on a disk.
Fortunately I run Linux (Ubuntu 14.10 since yesterday) and there's a tool called idl3ctl - one can grab it from here: http://idle3-tools.sourceforge.net/
I got the latest source code and compiled it myself because there had been some updates to it since the last release (2012 vs 2011 ..). "idl3ctl -g" shows that the disk was set to park itself after 8s. I disabled that with idl3ctl and powered off and on the computer and now the tool says it's disabled.
Hopefully this should increase the lifetime of my disk.