There are a lot of OTA's and aggregators around the world.
The most well know are Booking.com, Expedia.com, Kayka.com.
However, often you can find better deals on specific niche location by searching local OTA's and aggregators.
When I was in South Asia a few years ago I used a lot the OTA AsiaRooms.com (I think they have now been bought out by another company.)
When I am in the UK I usually use
http://Hotels-Fairy.com, they are a UK hotel price comparison website so you get rates and deals from UK hotels and B&B's that you don't usually find in the big OTA's like booking or Kayak.
On the other hand, when I want to book a flight in Europe or in Asia, Skyscanner.net seems to have the cheapest flights. However, you have to very careful with them when you book multiple flights as they are an aggregator and quite often prices tend to change when you go to the airline or travel agent website.
I hope this helps.
Regards
Nectarios