The E-bookers site, formerly flightbookers, was one of the first online flight reservations I have ever used, yet I have never actually bought flights from them. The reason for this is as follows:
I do not like the way E-bookers price fares on their site - you put in your origin, desination and dates. Then to your delight a list of VERY low fares appears. However do not jump for joy quite so fast as unlike some of the more competent systems (such as expedia and travelocity) which only return fares for seats which are available, ebookers returns all fares, and chances are there will not be seats available at the very lowest fares. The only way of finding out whether there is is to check availability on each fare yourself, which is a tedious task given that you will probably go through quite a number of fares until you get to one which is actually bookable, by which time you will have probably gone past the prices others are offering anyway.
Another problem is that you have to be a registered user and log in just to check availability - most other sites only require a login when you come to purchase seats.
In addition, they also have the nerve to charge £4.10 to send your tickets through the post, I know of no other online agency which does this (I know expedia certainly doesn't)
I haven't bothered using ebookers for a while now - there are no savings to be had and finding a flight with them simply isn't worth the effort.