Interesting topic and rather timely as I am in the midst of finalizing my plans for my upcoming trip.
Hotels: This upcoming trip the first I've used Booking.com. I have used a variety of sources in the past (i.e. Travelocity, Expedia, etc.) and have also found that booking directly through the hotel is sometimes cheaper...sometimes. But, I love the option to be able to change or cancel my reservation, if needed.
Flights: I prefer to book directly through the airline. Have never used a booking site (Expedia, Kayak, etc.) and right now...I may have to due to carrier issues with airlines from Slovenia back to the States.
Those of you who have used a booking site for flights - any issues? By any possibility is there a freedom to choose seats? If it was just me, the seat thing isn't an issue. But traveling with a parent who needs the much-coveted aisle could prove to be a challenge. I admit I'm a bit anxious over using one of these sites for flights and am hoping for a bit of ease of mind.