Have you thought about where you want to keep all your installed program software? On the data partition/drive, with the OS partition/drive or their own partition/drive?

I have two hard drives. The first has three partitions, a relatively small one to boot Windows XP, another small one to boot Linux (Fedora right now but I change it sometimes, I'm a dabbler), and the rest is a big chunk that I use for quasi-backup of my other hard drive. The second hard drive is where I keep all my stuff that isn't an OS or installed application (I have "My Documents" point there from windows, mount it to my home folder in Linux, etc). All of this is copied periodically to that extra partition on my first drive before backing it up externally.

I used to have another partition on the first drive for random OSes I wanted to play with (FreeBSD, other Linux distros I wasn't so sure about yet, etc) but now I just run all those in VirtualBox.

To be honest this is most likely overkill but for some reason I enjoy wasting untold hours installing and configuring and RTFMing, so in the end I can look and say "Wow self, that's once fine job we did setting up all that crap in that OS." The dual boot Windows / Linux thing is good for working on cross platform games, assuming I ever find time to work on one of those :)

I ALWAYS go with one partition per os.
Untill I was comfortable with linux installs, I made sure i used a different drive so i could unplug my main hard disks and not even risk overwriting something.

The key thing is that you will need to install your OS again at somepoint. Windows tends to get bogged down, and it is easier to just reformat and reinstall.
Or, the more likely case for most people, you just get a new machine, and want to move all your stuff over. It is really nice to be able to
*backup the windows data from the windows partition to the data partition
*then plop your old drive in the new box and reinstall the OS
*restore your data from the data partition.
Or:
*backup windows data
*pop drive in the new machine, restore windows data
*format the old drive's windows partition, and use it for data.

Both steps keep you from ever having to move your data (music, movies, games, pics, code). And if you have a TB of data, that takes a long time to move someplace safe.