Kayak
Kayak will scan across various airlines to give you just about every option there is to get from point A to point B. It is a great option if the price is a greater worry than time in transit.
Pros:
Will often find the cheapest itinerary possible.
Great for finding budget airline flights.
Has the capability to include airport transfers in the itinerary. (Ex: You fly from Boston to Rome, via London. While in London, you transfer from Heathrow International to Gatwick International.)
Will color coat across days on a green, yellow, and red scale based on the ticket prices for that day.
Is able to create multiple itineraries through different airlines to provide one whole itinerary to purchase.
Cons:
May have extreme layovers or airport transfers.
Itineraries may have multiple self-transfers. (This is where your checked bag isn’t sent all the way to your destination and you need to retrieve it from baggage claim and recheck it during some layovers)
Flight cancellations or delays when flying multiple airlines can severely mess up your travel more than when flying a single airline.
Ticket refunds through a third-party booking site can be tricky. (It took me a year to receive a refund for a round-trip booking to Sydney and Fiji because the flights got canceled)