I hope I don't get flamed for this since it is a frequent stay program rather than a frequent flier program, but I am convinced that the best program is Hilton Honors. Note that the primary methods of accumulating points in programs are the same in the airline and hotel industries.
A primary reason we accumulate miles or points is to get for free what would have otherwise cost a significant amount of money. The combination of the discounters, ridiculous airline fees and lack of award availability has reduced the value of the airline awards.
Case in point with Hilton. A person can reserve a $250 - $300 a night hotel using Hilton points and get the certificate. Up to the day of the planned stay, he can check for great internet rates and throw out priceline bids. If he gets the hotel for $75 a night, he can cancel the Hilton reservation and redeposit the points at no charge. Since it is easy to keep the points from expiring, he can always feel he gets $250 - $300 of value for the block of points. By the way, I almost always find availability at hotels using points.
Let's compare this to the airlines. You identify a flight you desire that retails at a significant price. If you find availability and book it, you are stuck. If the price comes down, you have to pay a big fee to redopsit the miles. Unless you are flying on Southwest, in which case there is no fee but the voucher expires in a relatively short period.
I know that many disagree, but I have come to appreciate the difference, primarily with respect to location, between nice hotels like the Hilton chain and hotel discounters such as Red Roof Inn - you never realize that many discounters don't provide complimentary shampoo until you are in the shower. I don't see the difference between discount airlines and coach on the majors. So that free ticket that would have cost $500 on the major airlines isn't really worth $500 if a discounter offers the same routing for $250. But the free night at the $300 a night Hilton really is better than the $60 Motel 6 four miles away.