Could you try to capitalize on the fact that you're right in between two enormous populations of PhD students and professors who are eager to both give talks and learn more?
Maybe you could support micro-publishing of books, or collections of interesting papers, for local distribution around Kendall/Harvard. Kind of like academic blogging but on paper.
Or you could host themed nights where a few academics give talks about why Subject X is interesting, and then you tell the audience they can buy/order books on Subject X from you at the end (and please do, it's how you pay for the free talk).
Also, I live right near Inman. You guys have the "Refrigerator Repairs" sign (or something like it) above your store, right? Hard honesty, from someone whose walked by many times and never gone in: the Refrigerator sign made me think you were a) too lazy to put up a sign for your store, or b) trying to be ironically lazy, which I think isn't a positive vibe to send to society. Either way, I transferred these impressions onto my expectations about the product waiting inside for me, and passed by every time. Perhaps that is a silly reason not to enter a book store, but at least it is a data point for you to consider.
Another idea: what if you provided a nice binding service for graduating PhD students. Package up all your papers and thesis together into a nice volume to show the kids one day. I know you can do this online, but you would provide nice Harvard and MIT themed leather book jackets with some stock material about the school or department history, along with a thicker page for the student to put some photos in from that time period. I would pay $100 for this. Maybe $200 if it was really nice. There's no class ring for PhD students, but this would make a similarly nostalgic memento.
Google Street Maps view:
Only issue is why they would come to a book store to do this rather than do this sort of thing at MIT or Stanford. Maybe, integrate a coffee/snacks/cosy reading room along with book store?
While I can't internet-verify it, one of my Spanish co-PhD students told me that in Spain you _are_ given a ring upon completion. It's supposedly to signify your marriage to science. I think my wife would have something to say about that...