A couple other sites have collected "great books" lists. The Greatest Books splits the aggregated list into fiction and non-fiction. More unfortunate still, it does not confine itself to lists of books from all human history. The creator of the site uses an algorithm, without telling us any details about it, to determine a ranking of the books, claiming to weigh all-time lists more than lists of books from the twentieth century or other periods. But he's missing many of the all-time lists, and moreover includes winners of several of the major literary awards: the National Book Award, the Costa Award, the Pulitzer Prize, the PEN/ Faulkner Award, the Man Booker Prize, and the National Book Critics Circle Award. These winners could be said to constitute an informal list of the best books of the period from which they were first awarded. But obviously those giving the awards were only voting for works published in a given year. We cannot conceivably say that one year's winner has been ranked higher than another year's. But if you go to the lists for each award, you'll see that those prize winners that are not on any of the other lists aggregated at the site nonetheless are ranked. That is, two books that are only included in The Greatest Books list because they each one an award (say, the Man Booker Prize) are ranked. So how does this site's author decide which winner of the Man Booker Prize gets a higher position? Alphabetically, by the title of the book! The author of the site also notes that for "the lists that are actually ranked, the book that is 1st counts a lot more than the book that's 100th." Without knowing what exactly he's doing mathematically, we can only surmise that this approach gives undue weight to the books ranked highly in the few lists (very few lists) that rank the entries. Now we've reached the point where the desire to rank the books, especially a large number of books, gets ridiculous; and why I prefer to avoid mathematical stunts.
Another site, A List of Books, features only two all-time lists, the Guardian's Books You Can't Live Without  and Newsweek's Top 100 Books, the latter being what its creators call a meta-list that aggregates several others. An article about that list is available at the Newsweek site (Building a Better List), but not the list itself; a subsequent search through some academic databases still has me stumped as to when and where that list was published. The author of A List of Books does not explain how he has aggregated the lists to get the number of points awarded each book.