They were a great, big, comfortable independent bookstore. They were right near the Menlo Park train station, there was plenty of parking, there was a good cafe next door (which is still there, but who knows for how long with the bookstore dead), and I loved going there with friends. I saw great authors read there: Ursula K. Le Guin, Jeffrey Eugenides, Diane Ackerman. I was looking forward to seeing Neil Gaiman read from Anansi Boys there in a month. They had online ordering and free local delivery. Their employees wrote mini-reviews of their favorite books and stuck them to the bookshelves. They had a very complete magazine department, too.
booksense.com, an association of independent bookstores, tells me that the next closest general interest independent bookstore (affiliated with booksense.com) is Books Inc. in Burlingame. But it's a chain with 10 locations, so not really the same thing.
There are still lots of great bookstores in the SF Bay Area. But - WAAH. IT'S NOT FAIR. [*stomps*]