Having run against section 508 rules just with plain old testing (for example with Cynthia Says), I have run into problems. These problems aren't usability problems, but issues like what Robert mentioned above.
If you are normally accessible- and usability-aware, as Alex said there shouldn't be any extra work involved (all your other sites have no excuse anyway : ), but there may be a bit of extra work checking for specific rules.
So, read the rules, make sure you're following them as you go. I'd love to say, follow WCAG2 (which basically just lays out scenarios that your site has to pass, technology-agnostic), but if you must be 508-compliant, you must follow it to the letter. The above-linked tool will check for the kinds of things a robot can check for, which helps. When you're finished, you may want to run your site past some other developer unfamiliar with your site to look for errors you cannot find because you're too used to the site.