Based on my experience, it's best to purchase tickets in advance directly to the airline or airline's website itself. I had enough internet fraud experience for this so I'm sharing this to you all so you won't get ripped off. As much as possible, stay away from those online agencies selling airline tickets for cheap prices.
Some of those agencies are legit. It's about doing your research, not just avoiding anything but the airline's website. If you look at the website and it looks cheap or flawed (ie., has a lot of advertisements, spelling mistakes, etc) or seems like it's way way way too cheap (ie., you are not paying taxes, fuel-taxes, etc), then maybe you want to back down. Also, check out customer reviews. There should always be favourable and negative reviews on every site.
Actually, I totally disagree with the OP. I mean, if people actually bought tickets directly from the airline, then they'd probably be paying thru the roof. Anyhow, though, I understand that online stuff can be a rip-off sometimes, but given the amount of money at stake, these big name travel websites have much to gain by being honest.
Well not all agencies are scams, so to avoid buying from one then you could simply just google the site's name to see if there are complaints from people that it is a scam or they have overpriced tickets.
We have been buying discounted plane tickets from a travel agency in the Travel Expo every February. Last year we bought 3 trips and this year we have bought 4 trips. The discount is 40% to 50%. Based on our experience, the agency is reputable. Next February, we are going to the Travel Expo again.