Keep in mind, that while installing to your second partition puts your program files there, you still have to reinstall the programs whenever you reinstall the OS.
The above being the case, why do so many recommend seperating the the OS and programs on different partititons? I've never understood what advantage it might be.
So many people recommend separating the OS from programs (as in program installation files), saved games, music, movies, documents, etc etc. If Windows gets hosed, it makes the reinstallation much less painless to have all the necessary files on a separate partition.
Also, not all
software will require a reinstallation, just the vast majority