If I have enough space,i prefer to partition the hard drive into two partitions:Macintosh HD A and Macintosh HD B
A: OS
B: documents, itunes library, iphoto library, downloads, superduper images of HD A, and Vmware fusion virtual machines.
I prefer to keep data away from the OS for a few reasons:
1. if there is a crash (even a hardware problem) if the data is on a seperate partition is is much easier to recover it than if it is intermingled with the OS. A corrupt OS can make accessing your data on the same partition very difficult. Likewise a physical problem (scratch) with a sector on the OS partition can make reading data on that partition impossible...if it is on a separate partition there is a better chance of reading it despite problems with the OS partition.
2. i can restore the OS on HD A in under 10 minutes by using a superduper image stored on B. This is a very fast way to restore your OS, a USB drive will be much slower by comparison. I do not need to worry about backing up my personal data with a few exceptions- address book, ical, bookmarks.
3. i like to keep the virtual machines on their own partition anyways. it keeps the file size of my superduper images of OSX small.
*I got into this habit because I come from Windows where being able to restore a machine from a Ghost image is a real time saver. I do not do it on my SSD equipped laptops due to limited space but with the 2 TB hard drive in my imac I do prefer it.