I am managing the development of a new web site for a Travel company
that sells flights and accommodation.  I am looking to find other such
sites on the web with an emphasis on user-friendliness, clarity etc. 
The main thrust of the new site will be the 'booking engine' which
will give the user flight/hotel/apartment prices, location and
availability.  Can you recommend some similar sites which would give
me some good design ideas?

Greetings.

Can't recommend any travel sites, per se.

However, if you need some input and critique on your site, you can try
these two forums.

http://www.cre8asiteforums.com
http://www.highrankings.com

If you ask nicely, people in the business will make recommendations on
how you can improve the effectiveness of your site.

Hope that helps.