There is a new organization recently formed called pilots n paws. It's a network of pilots that love animals. They are forming this organization to aid in rescue transport as well as alleviate stress on dogs/cats that have to take 16 cars cross country. These people are donating their time, gas and airplanes to make this happen.
You can donate, support or post your rescue on their message board. If there is a pilot going to your rescue's destination- they will contact you and arrange for transport. This is a great organization.
I also found these organizations as well, though don't know of anyone who has used them personally....
By air: http://www.flyingpaws.org/