Allow admins to close or suppress display of the yellow alert boxes that warn, for example, that "mod_rewrite may not be installed" or "wp-content is writeable [sic]".
Some setups require wp-content to be writable, and, when using a web server other than Apache, mod_rewrite is not applicable. Giving the user an additional warning before closing the alert permanently is perfectly acceptable if you feel you need it, I think, as long as the user can close them if she knows what she's doing.
(I have a lighttpd setup that uses lua to rewrite URLs for WordPress and redirects to cached files in exactly the same manner as mod_rewrite, and those warning boxes get kind of tiresome after a while. :))