Hi, I found this old topic about validating the HTML markup on the W3C for a whole website: http://csscreator.com/node/11210
I just wanted to announce a little tool we've released recently that allows just that, you provide a starting URL and it will scrape its internal links and validate them all (up to 100) on the W3C validator, producing a report. It also accepts XML sitemaps.
It's called W3Clove and you can find it at http://w3clove.com
I hope you find it useful.