This is an old question in a new world.
With an O/S and programs and any assorted data it made sense to have multiple partitions, Along came the registry with its admixture of O/S and programs and it made a mess of things for those who liked compartments. Some swore by a single partition for everything, and others just swore.
What are we to do with Win 7 and a clean install? (I expect a hundred opinionated answers, but that is exactly what I want.) Now we have Virtual Drives (and even a relief from that for XP Mode, Cloud Computing, and all the rest of it. What's a guy to do? This is not academic, as \i may reconfigure a computer quite soon.