I keep my program files and system folder on the same partition. Since the distance between them is closer that way, this should be speedier than having the program files in another partition.
Since you don't often change program and system files, it's easy to keep them unfragmented. Not so for the documents folders, which in winnt also hold the temporary (internet explorer) files and such. This is why I install those to a separate partition.
Data that don't change over time, like my audio-cd images, are kept in yet another partition. These don't fragment, but it would be inconvenient to put them on the system partition, since I reinstall winnt all the time...
Btw, you can tell windows at install time to put the docs+settings folder on a separate partition.
Hope this helps.