As of May 2017, the discussion is still valid, at least for certain types of hard disks and the old solutions are still doing the job. The trick is to set the power management level to less aggressive. On most disks
# hdparm -B /dev/yourdisk
will give you the APM (advanced power management) level currently set. You'll set it by the same command, with actual desired value.
# hdparm -B 254 /dev/yourdisk
Values range from 1 (the most aggressive power saving) to 254 (the least aggressive power saving). Values 128 and less will even allow spindown. 255 will disable APM altogether (not supported by every model). The level depends on the system's category (desktop does not IMHO need any other value than 254, and laptop... well either experiment a little or buy an SSD :)).
On Western Digital it gets more complicated. You either use the WD's utility WDIDLE3.EXE as in this post: https://ubuntuforums.org/showthread.php?t=1565889 or utilize hdparm again, this time with -J option (the specified values are in seconds to park the heads, read about the ranges in hdparm's man page next to -J option). The latter approach is less recommended, and does not work with all their drives.
I highly recommend to read this archlinux wiki page https://wiki.archlinux.org/index.php/hdparm where they discuss also how to make the change with hdparm permanent by making a udev rule in /etc/udev/rules.d/50-hdparm.rules
:
ACTION=="add", SUBSYSTEM=="block", KERNEL=="sda", RUN+="/usr/bin/hdparm -B 254 -S 0 /dev/sda"