I know for a fact that Hilton offers full hotel frequent guest program benefits through AAA.com, along with a few other hotel chains. Sometimes the rate is cheaper than Hilton.com, sometimes not. I usually use AAA, Priceline (regular and Express), ID90travel and compare them to the hotel chain's website and then see how much of a premium I need to pay to get points/stay credit. For me, I prefer cash in my pocket over a few percent in savings rebated in points.
On a related note, I was told by Holiday Inn (after an appeal to customer service) that even incidentals do not receive points if the room itself was booked through a third party. That seems a bit extreme.