My 5 year old compaq desktop came configured with 1 partition just large enough for XP (D

only and the other partition (C

for everything else. So far so good. My 2 new Asus netbooks arrived similarly.
That is a very odd configuration. In theory, it should work. The problem is that there are applications out there that simply will not work unless your app and OS are on the C:/ drive. I can think of one major antivirus that had this problem a couple years ago. Not to mention, you have to change every installation path for every application you install. That would be a nightmare for me. I would undoubtedly forget.
That said, it would make sense from a security standpoint. Many malware programs are going to look for
Windows on the C:/ drive. If it isn't there, it may cause the malware not to work correctly, who knows?
I, personally, wouldn't do it. Like I stated before, OS and apps on C:/ and file storage (My Documents) on the second partition. That would be my recommendation. By all means, do what makes you most comfortable. There are many ways to skin this cat.