WebAIM (Web Accessibility In Mind) is an excellent resource for information, tools, code, legislation, and more. They’ve written a great checklist for Section 508, breaking it down into what constitutes  a pass and a fail on each point.

The table is clear and easy to read. There are links to more information for individual issues. It’s also available in a linear (nontable) format.

http://webaim.org/standards/508/checklist

The checklist also includes descriptions for accessibility issues with plugins, scripts, and applets. However, this section doesn’t have a handy-dandy pass/fail column. You’re on your own there!