I'm using OS X and I see these ~ directories sometime appear my directories. I know Unix and I know that ~ represents the home directory, but these other ~ directories appear elsewhere and they aren't symbolic or hard links either. What's causing this?
It seems likely that some app is trying to write files to your home directory, but the programmer has been lazy and used the '~' shorthand in the code, which won't work, instead of
The thread Mysterious Tilde (~) Folder shows how to delete it, but it comes back later on.
The thread Mysterious Tilde Folder Appeared claims that this directory is created by Apple Software Update.
If that's really the case, then this is simply a bug in Apple software, and there is no way to get rid of it permanently.