When Borders made their most recent earnings announcement last week they also mentioned they're about to change their customer loyalty program. This PW article summarizes the new policy. I think they're heading in the right direction, but it's still not the best program for me.
After I spend $150 at Borders as a program member I'll get a voucher for $5 off a future purchase. The smart part about this is that it's a way to drive follow-up traffic to the store. What I don't like is that (a) it's not instant gratification like B&N's program and (b) it's about 3% off in total vs. B&N's minimum of 10% off.
That said, the Borders card is free and the B&N one costs $25/year. So if you spend $300/year at either outlet you'll come out slightly ahead with the Borders program than the B&N one. Double that to $600/year (which is at least what my family and I spend each year) and B&N has the advantage, but only by about $15, so it's not a huge difference.