There is a lot which you can do wrong when starting a new web site from scratch. The HTML5 Boilerplate project tries to help you there.
It contains a sane project layout, many useful JavaScript libraries, a default CSS that will make your page look the same on (almost) any device and smart CSS selectors that allow you to work around problems with browsers and devices which don’t behave well (small screen, IE6 bugs, no JavaScript enabled, you name it).