I guess there could be a speed increase if you're doing bandwidth intensive work which requires data to flow from one drive to another because of the fact that they're on different channels (if that's how you set it up).

I like to separate the very large programs from the system drive on my Windows installation, since the system disk tends to get fragmented a lot I like to install things on a separate partition which stays rather clean.

By the way, separating windows and your programs won't save you from installing them all over again. If you decide to reformat/reinstall you'll have to install them again because they won't be installed properly just because they're on a separate partition.