I was reading the thread about justfutoncovers.com and the sub-thread about getting a list of sites using jQuery, then I checked the listing page and saw MiamiHerald.com, well, as a developer for McClatchy Interactive (the owner of the Miami Herald as well as bunch of other papers), I am proud to say that most of our newspaper sites use jquery. When we transitioned the old Knight-Ridder papers to our platform, we decided to use jQuery to do some of the heavy lifting.
http://en.wikipedia.org/wiki/The_McClatchy_Company#Dailies We are also expanding what we use jQuery for all the time... so keep up all the great work everyone!