There is a kind of logic behind the way I've arranged these Online Agency lists, though this is such a blurry area, there is bound to be a bit of crossover between definitions. So I won't pretend it holds up to vigorous scrutiny!
First of all I've drawn a distinction between Online Travel Agents (OTAs) and Travel Agents Online.
I'm thinking of OTAs as those brands who are primarily online and have created a distinct online brand, eg. Expedia.com or Ebookers.com, which may have started out as a bricks & mortar shop (Flightbookers) on Tottenham Court Road in London, but is firmly a standalone online brand. As opposed to, say, ThomasCook.com, which I view as the online POP (Point of Presence) of the physical high street chain.
Then there are a couple of niches...
There's the Online Accommodation specialists; all those sites that sell "distressed stock" for the hotels like Lastminute.com, or Hotels.com, who clearly share a porous border with Price Comparison Sites like Trivago.com. And there's the Specialist Online Travel Agencies where I list all the other online brands that specialise in a particular sector, eg. Iglu.com (ski) or Railbookers.com.