I always like to drop a link to this validator when discussing bulk validation. Many do not know of its existence. I use it all the time. Almost every day.
WDG HTML Validator
You can either invoke the Validate Entire Site from above or go directly to a Batch Processing page. I prefer to use the above and go from there. That Liam Quinn does an excellent job of keeping that validator afloat. You can batch process up to 100 URIs at once. But, if they are rife with errors, it is going to stop at its predefined error count maximum. If you've reached that during a batch validation of pages, something is wrong and you should take a look at those errors to see what is going on.