Over the years, my preference for my hotel bookings has slowly switched from 3rd party sites (Expedia – mainly for its 6 miles per dollar promo with Citibank previously) to that directly from the hotel. This is due to progressively less bonus promo from credit cards (DBS Visa Altitude still has 6 miles per dollar promo) and more expensive hotels (Kaligo offers 10 to 12 miles per dollar but at a significantly higher price).
My preference further changed once I signed up for the IHG Ambassador programme which then make me choose IHG properties as my first option (direct booking with IHG). There are indeed benefits one can get from booking directly with the hotel (especially when you have status with them) e.g. my stay in Holiday Inn Munich. Another of my preference (but only if I will be staying for 4 nights) will be utilizing the Citi Prestige’s Hotel Night benefit (in which the 4th night will be free!). One can occasionally double dip on this privilege (e.g. for my upcoming stay in Osaka where I managed to book on IHG for Holiday Inn Namba using member’s rate, getting the points and get the 4th night free!).