Lots of subtle GPU rendering stuff that can easily give away a headless browser, or that differs between OS's in ways that can be used to detect when a browser doesn't match the expected behavior for the OS it reports to be running on.
Some of my favorite lesser-known ones:
'--install-autogenerated-theme=169,32,85', '--allow-legacy-extension-manifests', '--no-pings', '--no-first-run', '--no-default-browser-check', '--suppress-message-center-popups', '--ash-no-nudges', '--disable-infobars', '--use-mock-keychain', '--disable-cookie-encryption', '--js-flags=--random-seed=1157259159',