<<Is there an advantage in also creating a separate partition for all my other personal programs (as opposed to the Windows programs) so that I could back them up separately, or would it be better to include my programs in the C-partition with Windows?>>
Personally, I see no advantage at all to having programs installed in a separate partition...while I do see a possible nuisance. Windows seems to operate better if programs are where it expects to find them...and creating a second partition on the same drive results in slower access times between the two partitions.
But others have differing opinions
<<Is it in fact possible to back up and then restore programs separately since many will access items in the registry and might not work if the Windows partition has been restored as of a prior date?>>
That I have no answer for...I've never used any of my backups (full system partition backups) for anything other than to get data files or copies of programs which I want to install. (I don't backup because I'm reluctant to reinstall Windows...I back up so that I can have historical data or programs if I desire such in the future.)
As for restoring a program...I suppose it depends on the software used. I know that restoring individual data files was easily done by me, using Drive Image 2002.