maybe things have chined, but:
here's my experince: we took in august aflight from beijing to urumqi (nearly 3000y, because it was during the chinese's vacation and there were no discounts), from there a good express train to kashgar - david's info is very accurate! from kashagr we went on the back to urumqi through yarkand and hotan. the busses weren't THAT bad, but try to look for a flight back from hotan coz u can find cheap ones!!! we were also checkig about flying with the uzbeks, like enwhysea suggested, but: 1. they don't have a flight to kashgar/urumqi so u have to take another flight to kyrgystan or whatever stan u feel like, and then either take a third flight, or go "yabashtit", which mean having another visa and losing a lot of time! 2. the uzbeks don't have that kind of deals where you flight from one way and return from the other - which means that you actually buy a RETURN ticket to say bishkek (in kyrgy), and a ticket from beijing to tashkent for the way back in addition. bottom line is, that the uzbeks ended up being about as expensive as flying with el-al, and having another flight to urumqi, but take much more time!!! then again - maybe things changed in the last 2 years.