Unlike Booking.com and Hotels.com, Agoda does not offer transparent pricing. You have to click through to the end to see the total cost because Agoda intentionally leaves off fees and taxes. The problem, with these websites is that you will be given the worst rooms in the hotel. I used to use Agoda regularly, but found I was always, always getting the room that was in the back over the garbage bins, or on the side of the noisy road or in the worst part of the building. Booking.com would do that to me too. As for Hotels.com, I just went through an issue with a discrepancy with what was described and what was actually shown in the confirmation. It is finally fixed, but it took several weeks before it was. Hotels.com is Expedia and the service is atrocious. Look at the FT threads to read the horror stories about booking flights with Expedia, so you can have an indication of what the hotel unit is like.
I have used all these websites for Thailand, and to be honest, I am using hotels.com because its "reward" format is superior to Agoda and is even better than the so called loyalty programs of hotels like Accor and IHG. Often there is a price discrepancy with some locations and there are hotels which do not show up on the various websites. Look and then look again. Keep in mind that there is a conflict of interest with some of the review sites. Expedia owns Trip Adviser and Travelocity.
The one piece of advice is to look at all three websites and then at the hotel website. Sometimes the hotel will include wifi and breakfast whereas the OTA websites do not. Also the rooms booked at the hotels in Thailand tend to be in better locations in the building. I have booked over 100 nights in Thailand around the country over the past few years and that's my experience.