One very good independent travel agency I have found is the TV Travel Shop - a callcentre based agency that promotes itself through two channels on digital and cable television. TVTS has been successfully in business for about three years, has a huge market share in the travel agent business, and although HAS some special deals with particular operators (Cosmos, JMC etc) actuall deals with every tour operator possible! Most tour operators from UK also offer airfares which is one "cheaper" route for destinations that are popular with Brit tourists. For real airline fares, TVTS will also look at a company called Farebank/GoldMedal travel which is a flight consolidator, ie, buying seats from airlines and onselling em! Not everyone at TVTS seems to know about Farebank unfortunately, but if you want to book direct I think Gold Medal are based in Manchester. If you call them, you can then get the fare + named airline(s) and then check online if you can improve the price direct with the airline or through one of the online flight agencies.
HTH
