If you're planning a multi-city journey you can book all your fares on just one site (and often on one ticket with extended stopovers) with these sites. Some let you to book up to 10 destinations with one search.
Kiwi.com: Book up to eight flights
CheapOAir: Book up to six flights
STA Travel: Book up to three flights. (More can be booked over the phone or in-store)
Cheap Flights: Book up to six flights.
Vayama: Book up to three flights
I Want That Flight: Book up to 10 flights