When I go to Universal Access -> Hearing tab -> turn Visual Alerts on and try Test Flash with either the option to flash the window title or to flash the entire screen, nothing happens.
Also, see my related question about audio alerts.
As of Ubuntu switching to Unity ("3D") none of the universal access visual effects have been working.
Besides waiting for it to get resolved the only answer to this question at the moment is to use a version that does not use Unity. That would be Ubuntu gnome; or the still unofficial Ubuntu Mate. lUbuntu, xUbuntu, kUbuntu might be an option. Some will have different tool sets for universal access though.