Most websites like that are dynamic, driven by a database. For example, take Ebay. You see millions of listings, but they only have a few actual web pages (files that need to be backed up) that display that information. They query the database and display all those millions of pages. So for backup, the actual web page is probably changed, at most, once a week. That's pretty easy to backup. As for the database server, which is important, here is the typical backup plan. Do a full backup once a day. During the day, store and backup the change log to it. The change log can be applied to the full backup to re-create the changes for the day.
Disclaimer: I program a site similar to Ebay. We have about 200 distinct web page files that we backup daily. We have over 30,000 listings that change by the hour. The result is that, as a user, you will see 30,000+ different web pages that are changing minute by minute, but it is really an illusion. This is how we backup our website. Worst case, we will lose the last 5 minutes of changes before a disaster.
Trevor