From my experience with online booking agencies, there doesn't seem to be one that offers the best rates on all properties.

While trawling around trying to find info on hotels and prices, I've noticed that a particular company may offer great rates on some hotels, but their rates for other places in the same area are higher than other agencies' rates.
It pays to compare say asiarooms, asiatravel, sawadee and wired-destinations and see what you find.