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Using Momondo, the cheapest air fares are usually with booking sites like Fareboom, Travel2be, Way to Fly, Tripsta, Smartfares, SkyBooker, etc. Will airlines accept these tickets? What's the risk?

I have purchased tickets through Travel2be, Tripsta, Orbitz, Expedia and a number of other online travel agencies. Those are the same tickets, and they are issued by the airline - you get the airline confirmation code, and can use this code to check the flight status and do online checkin.

There is a risk because most of those sites do not issue you a ticket immediately. Instead you get a "booking number" and only then they try to confirm your ticket through the airline. This means you'll receive your ticket later - typically within 24hrs. However there could be cases where the airline doesn't confirm it, and thus the ticket couldn't be issued. In this case you get refund, of course, but if you need to fly tomorrow, you would lose time and opportunity.

Another difference arises if you need to change/cancel the ticket. This would take significantly longer as you need to call the agency which needs to call the airline. This might also cost you more than if you purchased your ticket through the airline, as those agencies often charge extra fees on top of airline change fees.

There is a risk because some may be illegitimate but I do it all the time. It is often more convenient and saves money to go through third-party booking sites because they can get volume pricing and special fares from the airline that are not available directly on the airline website.

Most of those sites sell genuine tickets that are booked directly from the airline through some kind of back-end. Sometimes they do a reservation which is booked later but most will send you an e-Ticket with Booking Reference within 24 hours.

What you have to learn from experience and by reading reviews is which ones are reliable. Generally, the ones established for a long time are good, specially if you are looking for the cheapest fares. Often the fare sold is not exactly the same as on the airline website and may incur additional fees for seat selection or baggage for example. In such cases, it did happen to me that after fees my third-party bought fare ended up higher than the airline one but usually not by much.

There are scammers out there and we have some questions here on specific ones but I would not expect many of them to appear in meta-search engines because the one doing the search normally has a relationship with them to get referral commissions. So if Momondo shows options with certain sites, I would consider the risk to be lower than directly on a third-party site.

Regardless, once you have bought a ticket and its booking is confirmed, you will nearly always be able to see it on the airline website. If they cannot confirm your ticket but your credit card gets charged, you can open a dispute with the credit-card issuer. So there is some protection there as long as the site does not ask you to use Paypal or a bank-transfer, for example.