This is a very interesting topic in my opinion since I were on both side and I still have doubt how I am going to deal with my every new laptop/desktop. However, I think I have a point for folks who want to settle this confusion.
Firstly, I never thought of using My Documents, My Pictures, My Music, and My whatever Microsoft named it. I think it's kind of stupid saving files in them because the real path is such a pain. From Windows 95 until Windows XP, it looks like this:-
C:\Document and Setting\<username>\My Documents
It's just simply too hard to type, remember, and use. I ended up storing things in somewhere like:
D:\<xxx>
Unfortunately, I still ended up with filling My Documents and mostly My Pictures with a bunch of stuffs because some programs--Office, all photo viewer or music management--just use those values as a default and changing the location every time is not fun at all. The real problem is when I wanted to reinstall an OS, I needed copy a backup of those directories. Then after I was all set with new OS, I just wanted those directories to be neat and clean, then waited until I had enough time to organize. Eventually, those sets of "My Documents" backup are still on the same place--never make it to where it should.
I might be like you, or not at all, but I really like what Microsoft have done with Vista especially Tablet features and how it organize all this folder. Their names are much easier to find and recognize:
C:\Users\<username>\Documents
So, I have less reasons not to follow this type of organization and surely I gave them a shot. Then, I'd better start previewing both solutions.
1. Stick with one: I believe that this is most people do because you don't have to do anything with it; just normal. However, if your system corrupted, it's over. That case doesn't happen every day though.
2. Better have two: This is what I believe it's so good since I mostly re-install my OSes every month--don't ask why; it's just fun maybe at that time--and use multiple OSes in the same machine--that's an obvious reason: I can't afford to buy 2-3 machines and learn them one-by-one. At that time, you have to remember that Linux could not handle NTFS this well, so FAT32 is just a practical solution; nonetheless, it has very bad limited which is a 4GB largest file. I couldn't bare using to store some image files I have. Finally the easy way is using FAT32 partition as a storage for every OSes. This way I have no problem finding files I want anymore and more importantly, OS crashes, breaks, or doesn't work anyhow; you just reinstall it. All your files are still there at the same old place. Don't think of more than 2 storage partition, I don't think it's a better solution.
Up to now, it seems that one dedicated partition for storage has only advantages over a single partition. Let's see why single partition is more than enough nowadays.
By the way, do not think I'm convincing you to use this way. I'm okay with both, but these days I need my machine to be more reliable than before. I am not dare to play with every stuffs I possibly find; I'm so tried of installing any OSes every two weeks or month. So this is the way I believe it's good for me now. Just so you know, I run Vista Business & Xubuntu on my X61T, my data are mostly in Windows' partition, it's working beautifully like my old days with many partitions. All in all, if you want your data to be safe, both ways are the same, but you can increase reliability of your data by having a backup.
The problem is choice...you decide it