partition (Where operating system is installed) is usually target
for viruses, bad sectors, out of disk space (Which is quite common in
Windows Vista and the next versions due to the winsxs
folder's uncontrolled size increase) specially in Windows. You may
need to re-install or
even format your entire system partition, in situations like this the
problem is how to backup your data if your haven't lost it already!!
Although it's possible but it's not easy, Unlike Linux , Windows does
not have any official live CD so you would have to use command line or
connect your disk to another system and wait until it backups your data
and then you can start re-installing Windows, it's a very time consuming
process and not every one has multiply OSs or PCs.
different disk for users' data can also improve performance in Multi
Tasking. Also If you're a Linux user there is another advantage. Using
another partition for users's data allows trying other distributions -
which is quite common among Linux users - without having to be worried
about data loss.