Very true about Agoda.I have used them many times,but the first price you get does not include,tax,service charge,etc.
Used to be that the booking sites were cheaper than booking direct with the hotel.But I guess the hotels have wised up and have started doing promotions(early bird,room only,etc)
If you've already got your flight booked ,it's best to check the prices of the sites and the hotel website on a daily basis.You'll get the best price,especially well in advance.
For example,I had booked my flight for August,and I was checking prices for the Grand President for a deluxe suite.On Agoda it was 2700baht(plus those hidden taxes/charges),and at first it was 2500baht direct with the hotel website.But after waiting and checking daily, a "Time Deal" for the same Deluxe suite,room only(try getting up for breakfast when you've got last night's spinner next to you) for 1600baht per night including taxes etc.
Good things come to he who waits ;)