No Question about the good point of having partition.
Lets now talk how big should be a good partition. Now these days its common to have 320Gb Hdd so, will 2 partition be good?
I saw a thread discussing about fragments, yeah we know it bu how much will be the ideal partition.
I suspect the your CCleaner is not for enterprise use.
Most of the applications will not run on server OS.
I am also thinking that your server is 64bit.