I've used many hotel sites : agoda.com, hotelclub.com, hotels.com, booking.com, ctrip.com. All of them are trustworthy. The prices are pretty close, though sometimes agoda.com and booking.com have better prices, and ctrip.com is sometimes cheaper for China hotels.
My favorite is agoda due to its consistent low price, user friendly interface with reviews, map, hotel facilities, room amenities all easily available. Makes it easy to choose the hotel. But I fall back on the others when I can't find anything good on agoda. I usually check hotel reviews on tripadvisor.com as well.
Like all internet bookings, sometimes they will screw up and you might end up without a room despite having a confirmation. It's inevitable since they book thousands of rooms a day worldwide so will make an occasional error. So I usually followup a booking with an email to the hotel directly just to be sure.