I myself use Wordpress.
(Now don't you go 'bah! wordpress!? FEH!')
WP started out as a blogging tool but nowadays is on-par with many CMSs.
On the customization front: It supports themes. Your own, or others, or mods of others. It even has a theme editor where you can modify the css and php files of the current theme without having to DL, edit, and upload it all back.
An example:
http://otakaos.110mb.com/
(Be sure to hover your mouse over certain elements, as they have some pretty nice effects, achieved without the use of flash.)