There are a myriad of reasons to do that. I do it to give myself modularity. I want to reinstall windows? Delete the windows partition and install. Same for changing motherboards. I want to buy a new drive to complement one I have to make a RAID 0? Pop it in, move the programs/games partition over and change the drive letter. Messed up or got hit by a virus? It's stuck in one place. etc. etc.
Right now, I've got a 40ish GB XP partition, a 60 ish Win764Pro partition, a the rest of the terabye partition which is the programs games one atm. And a 640gig AAKS WD hard drive which is my data. I used to have both windows partitions on an old raptor, but they're now on the samsung spinpoint f3. The programs/games partition was on a RAID 0 with two 160 gig drives.