The "tilde" files are the previous version of the file. In other words, if you had a file that contained 10 lines of text, then removed 3 lines, the "tilde" file would still contain all 10 lines.
This is actually an incredibly useful safety valve in case you screw up an important file like XF86Config or fstab or whatever. These files are not being created on any sort of scheduled or automated process, they are created when you edit and save a file. -- J.W.