The user can customize fonts, colors, positions of links in the margins, and many other things! This is done through custom Cascading Style Sheets stored in subpages of the user's "User" page.
E.g. To create your own CSS modifications for the skin you are presently using, create a page at Special:MyPage/skin.css containing the CSS you want to use (to apply your changes regardless which skin you are using, put them in Special:MyPage/common.css instead). For how to hide particular messages, see WP:CSSHIDE.