I can vouch for booking.com and agoda. Used both a lot. No problems with either site.

With Agoda, my wife once booked a hotel in Thailand that is really far from the city. Only found out when we arrived at the hotel. Not Agoda's fault since they did have a map. It was our first time there and did not know that the hotel is really far. Upon arriving in the hotel, we asked the front desk if we can cut our stay to 1 night instead of 3. They told us to call Agoda and check with them since it was prepaid. She called Agoda, they agreed to cut it to one night and moved us to another hotel in the city center. Just had to pay a small difference between our prepaid hotel room and the new hotel rate.

With booking.com, you can choose to pay upon booking (cheaper option) or choose a booking that can be cancelled. If you choose the latter, you will need to provide a credit card but they wont charge it. Have done it a lot of times with no problem. Except once I had the experience of cancelling a booking. They confirmed it was cancelled. The hotel had a screw up. The hotel charged me one night for no show. Called the hotel and they denied charging my card. Emailed booking.com about the problem. Also called my card and disputed the charge. After a few emails, booking.com had the hotel (holiday inn zurich) refund my card of the wrong charge.

For pricing, just compare the 2 for whoever is cheaper. If you are not comfortable with either one, you can always use travelocity or expedia. No experience with hotels.com