We have flown all three out of Buffalo - our favourite is Southwest for two main reasons - if you need to change flights, there is no fee, and their non-stop flights stay non-stop flights. I have booked with Airtran several times as a non-stop flight, and had it changed to connecting, and then had to wait two hours for a late connecting flight - not fun when you're wasting precious WDW time! Also had to pay $75 to change to an earlier flight time last year - ouch!
Jet Blue we flew for the first time this past June and were very pleased with them - kids enjoyed the two-by-two seats, the tv's to watch and the full-size pop and snacks to choose from. On-time flights and no problems at all.
Our favourite is still Southwest - have a flight booked with them this November! I did book AirTran coming home, only because it was $30 cheaper, they have ME check-in, and they had a later afternoon flight that Southwest didn't.
Hope it helps!