You'd use a small partition on one drive for the OS and whatever you need on the other drive for applications. The rest could all be converted to data storage partitions.
For the most efficient use of the drive you'd also want the OS and apps to only utilize 50-80% of the available space on thier partitions. This allows the smoothest operation of defrag.
Splitting your Windows applications and your Program Files strikes me as a very poor idea.
Almost all of the major windows applications, when installed, dump things into BOTH the "Program Files" folder (which you suggest putting on a separate drive than Windows), AND the Windows folder (or the Windows\system(32)) folder PLUS the Documents and Settings folder.
In other words, once you install Adobe Acrobat you've got Adobe files littered across two partitions.
Then, when you've got to do a backup or restore, the Adobe files are going to be out of sync.
There are very very few Windows programs out there that really don't touch anything outside the Programs File folder, meaning that you can't count on the software working after backups and restores. Plus now you have the hard drive head flying all over the hard drive to load programs.
I would therefore never recommend installing Windows applications onto another partition away from your Windows installation.
-Llama