I read with intrigue an article submitted by a friend:

Explanation of Ubuntu Hard Drive Wear and Tear
It says that from Feisty onwards, Ubuntu has been using the hard disk’s power management feature to spin down the hard drive, in an attempt to save some juice on your laptop battery. However the powering down of the hard disk is also contributing to hard disk’s wear and tear. I would say that this feature is not that useful in a desktop, since power is abundant. This is the suggested workaround:

hdparm -B 255 /dev/sda
I don’t know whether the author means for this to be included in the /etc/hdparm.conf file, or to be run in the terminal. Whichever it is, it’s worth a try. I have yet to try it.
Meanwhile, I went looking for some explanation on Google, and some say that this problem might be a bit over-rated:

Is it true that ubuntu can damage hard disks!
Thousands of webfarms are purring with Linux installed in them, why has nobody raised the question of hard disk crashing yet? This might be an isolated problem, but a problem for us Ubuntu users nonetheless. We’ll just have to wait and see.
As for me, I’m getting that external hard disk casing soon. To backup all my stuffs, just in case!