Ah yes, this is one of the big secrets that many soon-to-be published authors don't uncover until they're published: distribution (and print run) are king. In many, many ways, much of the success of a book is determined long before it hits shelves, and is up to a team you might not even have thought much about - the sales team.
Here's what happens: you write your book, you and your agent deem it genius, you and your editor deem it genius, and then...from there...a lot of it is out of your hands. Hopefully the art dept gives it a fabu cover, and hopefully the marketing and PR team come up with an incredible campaign, but what really has to happen is that the sales team has to believe that this book can sell the hell out of itself, and thus, when they take it to Barnes or Borders or Amazon or Ingram or Target or Walmart, etc, their buyers want to place big orders. If the sales team just isn't as jazzed up as it needs to be or if they can't sway the buyers to place big orders, your book simply isn't going to get in enough places to make much of a dent. You can hustle the hell out of it and if buyers can't find it, well, they can't buy it now, can they? (I would say that this might be the single biggest complaint you hear from published authors - that no one can find his/her book, and if you feel like complaining, just know that you have company on this one.)
As far as what really makes the biggest hit, in terms of sales? Yes, Target, Walmart and Costco are biggies. In fact, I was just informed that Target placed a big order on the paperback of TOML and named it a Breakout Book from Aug-Oct, and my team (ugh, not to sound pretentious) is jazzed. Because the support of one of these biggies can completely change the trajectory of your sales and your success. That said, can you hit a best-seller list without it? Well, sure, my hardcover did, but you still need a strong distribution throughout the major chains (again, up to your sales teams and the store buyers). There are few things more frustrating than getting great reviews and great press and knowing that people WOULD buy it if they COULD find it, but since they can't find it, they forget about it, and voila, there goes the momentum that a prominent review might have held.
So how do buyers make their decisions? I'm not a buyer, but from what I can tell, it is partially based on previous sales, partially based on trade reviews, partially based on the amount of support and $$ that your publisher is throwing behind you. So they place an order, and these cumulative orders determine your initial print run. If Target or Walmart decides to place a biggie order, it can significantly boost your print run and generate a ton of enthusiasm which trickles down to your entire team...and thus, might help them sway other buyers to place bigger and better orders.
As far as Amazon, I think it depends on the book. I found that Amazon orders made up about 15% of Time of My Life hardcover sales. But then, I had strong distribution in stores, so maybe people preferred to literally get their hands on it when purchasing. Others might find this percentage higher if their book is harder to find or lower if their book is available everywhere (airports, grocery stores, etc).
It's funny to realize how much of this process is out of your hands. Well, maybe funny isn't the right word for it. :) But so much of it depends on outside factors: what buyers think will sell, other books that are launching the same month that yours are, how much marketing dough they're throwing your way, etc. I guess my advice is to go into it with realistic expectations: almost every author I know (barring the biggies) has gotten those emails saying, "I want to buy your book but can't find it!," and it is so, so frustrating, but it is simply how this game is played. Hopefully, your sales team is doing a kick-ass job (a HUGE shout-out to mine for landing me Target - I freaking LOVE THEM!!), and that's all you can ask for at the end of the day.
Other authors want to weigh in? I'm sort of fascinated by this subject.