After reserving a hotel room with Booking.com I booked my flight via Expedia and was offered the same room for approximately 10% less. Numerous mails to the customer dissatisfaction team at Booking.com confirmed that there is no interest to handle complaints in a proper manner and the "best price guarantee" is worthless.
My advice, do not simply assume that this comparison site will result in you securing the most favourable hotel rates. Shop around and do your own comparison.