I would always say keep them on a drive separate from your operating system and application programs (even if that separate drive is only a second partition in a single master drive), and back them up on an independent drive as well.
I always create (at least)2 partitions on my master hard drive, so that the operating system treats them as 2 (or more) separate hard drives.
I only ever store the operating system and application programs on the C: drive, then store all my data files (pictures, music, documents, etc) on the other drive(s) [ D: drive etc. ]
I usually also have an additional internal "Slave Drive" to keep a backup of my data files.
This means that I can easily reformat the C; drive and reinstall software in the event of major problems, without worrying about saving my data files first. It also gives me a high degree of certainty that my important data files will not be lost in the event of a catastrophic hard drive failure.
I'd keep files that im not sure i want to keep in the 'downloaded' file on the computer. Any pictures I have i put in the 'pictures' file. If you know for certain that you want to keep a program, just store it in the 'desktop' file.