Well, moving them would do the same job, but whether you move them or rename them it would be difficult to do them all simultaneously with the command line. This is because *you* have to decide which ones to move or rename, it is your call.
However, if you wanted to rename all the files in a directory by appending a "~" to the file name,
for i in $(ls); do mv $i $i~; done
would do it.
If you do decide to rename them, if you rename them by prepending "AA" to the file name so that "file1" becomes "AAfile1" and "file2" becomes "AAfile2" then when you list them these files will appear at (or near) the top of the listing.
If you rename them by appending "~" to the file so that "file1" becomes "file1~" and "file2" becomes "file2~" then they will remain in (or near) the same place when you list the files.
This will be the same for directories or files, of course.
It is simply a matter of preference. Moving or renaming will have the same effect, do whatever you feel most comfortable with, just make sure you can easily revert to the original file name or directory name if you have to.
And my apologies, I seem to have mixed up append and prepend in my previous post, I think I have them the right way round now