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I typically generate css with php, usually in the header but sometimes in a linked file. Using this method I can easily alter site wide color or fonts, etc or feed the style atrributes from a database. This method also allows me to create blocks of css for different page elements and include them as needed - forms, menus, etc - or dynamically include definitions when conditions are met. This offers a lot of flexibility in terms of organizing and making changes to the css.