On the hotel side, most of the hotel programs will not allow you to earn points with third-party reservations. As importantly, you'd be surprised how often the reservation simply "disappears".

A few years back, when I worked in a Hilton-brand hotel, we actually had a procedure to deal with the situation, it happened so often. The third party would book a "block" room with no name and fax (yes, fax!) the guest information to the hotel.

It's so easy to lose a fax...