Found another one: ~/Library/Caches/com.github.atom.Shipit
NOTE: in a post above, the path’s with spaces were quoted improperly.
So, the new “complete” list becomes (with proper quoting):
rm -rf ~/.atom
rm -rf /usr/local/bin/atom
rm -rf /usr/local/bin/apm
rm -rf /Applications/Atom.app
rm -rf ~/Library/Preferences/com.github.atom.plist
rm -rf ~/"Library/Application Support/com.github.atom.ShipIt"
rm -rf ~/"Library/Application Support/Atom"
rm -rf ~/"Library/Saved Application State/com.github.atom.savedState"
rm -rf ~/Library/Caches/com.github.atom
rm -rf ~/Library/Caches/com.github.atom.Shipit
rm -rf ~/Library/Caches/Atom