Just leave it to the default

I remember when cluster size optimization was important back when we had 20 mb hard drives.

With 250gb hard drives going for $80, you're better off focusing on tweaking something else on your computer.

In terms of disk I/O, the parameters you should really look into is rpm, built-in caching, as well as what kind of interface technology its using (i.e. SATA, Firewire, USB 2.0, IDE, etc.)

Regardless, partitioning your HD was a good move, leaving the OS in its own partition should help minimize fragmentation.