I had this "wonderful" essay about book buying, but I'm still waiting for Tin to publish it, so right now, all you need to know is that book buyers determine what books bookstores order and in what quantities, and isn't far off from what a comic book retailer does when he or she isn't manning the counter.
For big bookstore chains like National Bookstore or Fully Booked, it was highly unlikely that regular customers could influence what books they stocked. Sure, you could place orders on specific books, but when that book actually arrives, you're the only one who receives a copy of that book.
My experience with A Different Bookstore was different. At the time, I was making good use of their book ordering system. Ordering books from A Different Bookstore isn't any more expensive than ordering books from, say, Powerbooks, but what I liked about it is that the books arrived faster. It averages out to waiting for a month for regular books to arrive (more if it's a "rare" or hard-to-find book) but there was a time when a book order arrived in just two weeks. (Of course knowing when their new stocks arrived also helped me "place my order" at the optimum time frame.)
Because I had similar tastes when it came to the kind of books they ordered (i.e. the fantasy/sci-fi genre), it shouldn't be surprising that they were learning from me as I was benefiting from them. Some of the books I ordered made it to their shelves instead of simply the lone copy of the book I ordered. An example I think was Jeffrey Ford's The Fantasy Writer's Assistant and Other Stories. Now I'm a big Jeffrey Ford fan but his books aren't exactly mainstream. In the five years since I last read about him, there are only two other bookstores that stocked his books in at least one point in time, and they're both independent bookstores (Aeon Books and Booktopia). So when I ordered two copies of the book, A Different Bookstore didn't just order two copies. I saw around three other copies at their Glorietta branch and at least one more in their Podium branch. (And thankfully, all those copies sold out.) It's always possible that they ordered it out of their own volition, but I find it coincidental for them to stock a non-mainstream title (especially when their fantasy selection comprised of authors like Margaret Weis, Raymond E. Feist, Robert Jordan) at the same time my order arrived.
This was all possible, however, because A Different Bookstore back then was operating as an independent bookstore (albeit one with bookstore chain book-buying habits--what you see in one bookstore, you'll see in another branch).
Of course being an independent bookstore similarly allows you to take a risk and learn. When it comes to D&D RPG booksfor example, I don't think anyone (not even the gaming shops) really mastered the optimum way to place orders until it was too late. Simply put, bookstore book buyers don't know which RPG books to order and in what quantities. Of course of all the bookstores, I think A Different Bookstore fared best (especially when they stuck to the formula of ordering The Player's Handbook, Dungeon Master's Guide, and Monster's Manual instead of the other supplements or -gasp- adventures). It's only when they drifted from this formula that things started to fall apart and books like Shining South, a $30 hardcover, ended up selling for $2 at the book fair.