Comfort comes in two flavors:
1) Amount of leg room and seat width in an average coach row
2) Amount of seat padding and structure of seat to provide lumbar support
Jetblue is best for #1, but not for #2 on A320 aircraft (OK on E190's). Jetblue A320's have very thin padding and are not the best for longer flights. They also use a tilt mechanism that does not give great support for the lower back.
I agree on Virgin America being best overall - they fly mostly coast to coast and up and down the left coast. Great seat pitch, width, and padding/support.