Due to popular demand (and my general dislike of interaction between image changes and caching, plus a rash of vandalism of a certain type) I've added two new permission keys to limit uploads that overwrite existing images.
Disabling the 'reupload' right will prevent any upload of a file which already is present, either locally or on the shared repository (Commons).
Disabling the 'reupload-shared' right will prevent overwrites of images which are present on the shared repository but _not_ on the local wiki. (A pre-existing local image overrides the Commons image.)
For fun I've set the default message to display a thumbnail of the conflicting image on the error page like so: http://upload.wikimedia.org/wikipedia/meta/3/3f/Upload_restrictions.png
Currently, reupload-shared is set to off for regular users on all Wikimedia wikis, but the general reupload right is left on so local images can be overwritten (and images on Commons can still be overwritten there).
The message can be customized/localized at [[MediaWiki:Fileexists-forbidden]] (for local images) and [[MediaWiki:Fileexists-shared-forbidden]] (for Commons images)
-- brion vibber (brion @ pobox.com)