After 8 seconds of inactivity the disk parks its heads. Gives slightly less power consumption while the disk is idle and it's great for a storage drive if you ask me (some do disagree though) but it can be very annoying in some cases when say the disk is accessed every 10s or so.. Sometimes the OS cannot leave the OS drive alone, resulting in constant unloads and reloads of the heads.
There are AV versions of the WD Green which don't have the head park feature (or it is disabled), designed for constant-on operation. We used these in our various Home Server build guides a year ago, and they are excellent. http://www.silentpcreview.com/Silent_Ho ... uild_Guide
Besides, I wouldn't use a 5400RPM HDD as an OS drive anyway, as they have slow seek times. An SSD + a WD Green would be perfect. If your budget doesn't allow that I would go with a 7200RPM drive for OS and storage, or if you don't mind having OS/apps on a 5400RPM HDD, choose another one without the head park feature. I like the Samsung F4 but I hear the new Hitachi is good.
Agreed that an SSD + big WD Green (or similar high capacity HDD) is ideal. It's what I run on several PCs. But... while the random access time of lower RPM drives is naturally slower than 7200rpm drives, the difference never seems that significant to me, and the high areal density of today's drives makes throughput very similar for slower/faster rpm drives. In any case, one simple way to speed up a HDD is to make 2 partitions, first a small one (say 100gb) for the OS, and a second of partition of the rest (1.9gb) for data. This means all the OS operations happen in the fastest outer edge of the disk, effectively improving performance. I've done this on single HDD HTPCs, and have no issues with performance.