As a web developer, a number of the projects I work on fall under government umbrellas and hence are subject to 508 Accessibility laws, and sometimes W3C accessibility guideline
If accessibility is your primary concern, always start a website using standards-compliant (pick a Document Type Definition and stick to it) HTML. If it's a web application (form submissions, etc), make sure the forms will work using just HTTP GET and POST. Once you have a complete website/application you can add bits of CSS and JavaScript as long as the site still functions, with either or both off.
The most important concept here is Progressive Enhancement. You're adding additional bells and whistles using CSS/JavaScript, but your web site/application will function perfectly well without either.
A great tool for testing 508, WAI, CSS off, JavaScript off try using the Web Developer plugin for Firefox.