Here are the contenders:
Amazon Reviews: Upside: Tons of traffic. Rating the raters in terms of helpfulness and having a top 1000 reviewer list both give incentives for people to take their ratings seriously. Plus, most serious internet users already have Amazon accounts with demographic info, so they don't have to pressure people into joining. Thus all rating requires is one click. Downside: Amazon's team has all the tools, but they just don't seem to want it. They're like the Carmelo Anthony of online book rating. They don't really take their rater's reviews seriously, they refuse to expand to a much more informative 10 star system and they don't give out actual numbers. According to their system, The Shawshank Redemption VHS Tape is the #6 best book of all time. Listen, I'm willing to accept Amazon has much bigger fish to fry. They're trying to take over the world, after all, and they don't have the energy to create a silly top books of all time list. But what that means is that although Amazon may be the best right now, the true Holy Land will have to be found elsewhere.
The Internet Book List: Upside: Pretty solid system in place with cool ratings breakdown on a book by book basis, and a large emphasis on the actual ratings, which is basically the only point of the site. Downside: Scale! The most rated book on the site is Tolkein's The Fellowship of the Ring, with 541 votes. Compare that to the 5,100 who rated HPGOF on Amazon, or the 440,000 who have voted on Shawshank on imdb. Some of this is inherent to the medium, as it takes more time and effort to read a book than it does to watch a movie. But there are more book readers out there than 500, and in order to get them to the site there's going to have to be some other kind of attraction aside from the ability to rate. Of course, the internet wouldn't be in a Nash equilibrium if building online communities were easy. I recognize that achieving scale is tough.
ISBNdb.com: Upside: Tons of web crawlers on various library web sites have created a massive database that categorizes books by subject and offers a link to the lowest possible price. It's a very cool tool, and tries to explicitly model itself after imdb. Downside: No actual rating system. Included in the list anyways because that isn't the hardest problem in the world to fix.
Metacritic Books: Upside: Standard metacritic methodology applied to books yields a solid if unspectacular rating system. The opinions of critics may be slightly better in some ways but never enough to outweigh the benefits of pure bias-defeating scale. Attractive interface, easy to browse web-site, and a best of all-time list, in theory. Downside: Stopped aggregating ratings for books in 2007, presumably because it wasn't profitable. This raises some troublesome questions. Most importantly, why do people seem to care less about the ratings of books than of movies? One has to put such a big time investment into reading a book that from a time-optimization perspective research into its quality would be of huge value. Anyway, metacritic's book rating section is done. Put a fork in 'em.
Complete Review: Upside: Breaks down the top books into tiers by categories. Editorial board is willing to take a stand and submit their independent opinion. Downside: No user input and the lack of a quantifiable system means that it will never scale. At best, it's another data point in a more encompassing effort.
Reviews of Books: Upside: Aggregates reviews by various important book reviewers and gives details regarding nominations for major prizes, like the Booker or the National Book Award. Downside: Nothing quantifiable. No overall list of the best books.
Internet Book Database: Upside: Rank authors, books, and series's, according to both number of votes and average rating. Has some good ideas for how a website ultimately could be done, despite technical issues. Downside: For some reason they've bought into the stupid Amazon model of 5 star rankings. Just like Amazon they don't give the actual numerical average rating. But they go further and don't even show the total number of raters. This makes me uneasy about their methodology--does the site even weigh the top rated authors by the number of votes in a Bayesian fashion? Moreover the lack of transparency is troubling--it's hard to tell where exactly their data comes from. The fact that Lara Leigh is apparently the #2 author of all time yet doesn't even have her own Wikipedia page lends legitimacy to these worries.
LibraryThing: Upside: Lots to like here. Tons of statistics on books and authors, including the most highly rated, the most reviewed, and the most number of times a book appears in a user's library. They actually show the numerical rating that a book gets and the pages for individual books are useful. Since they allow half stars and allow us to see the actual numerical rating, I can't even really complain about their use of a five star system. Downside: A little bit too hipster in that they refuse to actually number their lists and seem to be going for the minimalist look. But hey, if it gets raters, that's all that matters, right?
All of these sites may one day blossom into something useful. If it's legal, there would be value in some site aggregating all of these ratings plus a few others to become a meta-rater. But for now, I'm still searching...