For me, B&N all of the way. The stores themselves are more serene, better stocked, better organized, and the employees are a lot more helpful and knowledgeable. The cafe is Starbucks, so no complaints there. They also have a faster ship time when you order things.
They carry textbooks, and they have better rewards. For example, I just got a $25 book for 45% off with my membership card and a coupon. Their coupons are always in addition to other discounts on the book, unlike borders who does it in lieu of any discounted price existing on the book, so I use it more. They also apply the coupon to the most expensive item, unlike borders who takes it off the least expensive item.
Sure it costs $25 a year for membership, which is my birthday present to myself, and I easily earn enough in discounts to pay for it within the first month by textbooks savings alone.