These are backup files created by some GUI editors, like gedit. You can:
1) disable the creation of the backup files, from the editor's options
2) enable the file manager to show backup files
3) remove them all in a single shot:
Code:
find . -name \*~ -exec echo rm {} \; # the echo is for testing
If you don't feel the backup files are necessary, you can apply points 1 and 3 above.