Personally, I keep everything on one partition. I image the hard drive
one time, then make subsequent incremental images. And for me, it's just
as easy to keep track of everything on it as it would be if I created
several partitions.
But some people like keeping data in a separate partition. As long as
they regularly back it up, that is a good strategy, too. And this way,
when they image C: (which would contain the OS plus the programs), it
(the imaging process) doesn't take as long. And if they were to restore
that image, again, it wouldn't take as long.
If you decide to install programs to a drive other than C:, the above
strategy falls apart because when one restores the image of C:, the only
absolute guarantee it will work 100% is if the image of the other
partition that contains those programs was done at the same exact time
(because of how installation routines almost always wind up altering the
C: drive in numerous ways). What one could do instead is image the
entire hard drive (i.e., all the partitions). But borrowing from what
you just said, "using that logic, why have more than 1 partition at
all?"

(And that is why I prefer to use only one partition on my hard
drive.)
Actually, this article by Ken explains it much better than I can

:
http://www.computorcompanion.com/LPMArticle.asp?ID=326