There are times where I find myself sorting out itineraries, only to be told "I have seen this-that-or-the-other on this or that website ..."
Many online agencies may offer cheap alternatives. Question is, are they any better when you consider other factors?
The actual airline performing the trips may be an issue. Some airlines travel through places where you need a visa - not a problem if it is a fast transit (as long as you do not need a transit visa, of course) BUT if you get stuck in such a place, then you are confined to whatever transit lounge is made available. If the airline is a bit of a one horse wonder, then that may be for some time. Examples are places such as China or India.
Length of stopover should be considered. These waiting times are not always taken on board by many clients. They are, sometimes, written in rather small print. What looks like a good deal, may have the shine taken off it, when you find that you are going to have to wait 17 hours at an intermediate airport.
Length of flights are important. There are some quite plausible routes though they may involve going the wrong way before you set out on your actual journey. Turkish Airlines, for example, offer some very good deals. Great if you are heading East, not quite so great if your itinerary goes West.
What are you actually saving? A recent example to Johannesburg involved going via Dubai - a break in journey which saved £50 - on a fare of £700. Emirates are, of course, an excellent airline though one wonders if it really worth while adding in the extra stop (and an extra 3 hours or so) on a 10 hour journey - Does that equate to a *worthwhile* saving? My own view is that unless the saving is greater than 10% of the fare, stopovers wont simply cut it.
Whenever you are considering a trip, before you dive into finding the best online agency for this or that combination of flights, I suggest that you start by looking at the most direct service on whatever airline serves your chosen destination, first. This is for two reasons. Firstly, you may well be surprised at what a direct airline may be able to offer and secondly, it provides a useful benchmark for you to decide if using an indirect service is really worthwhile.
And finally, remember - many online agencies are not actual agencies; they simply take information from third parties. I wish I had a Dollar for the number of times where I have followed through some request, only to find that when push comes to shove - Guess what? The online price changes to what I am looking at - or more than what I am looking at - on my Sabre system!