I had a new experience yesterday. I was flying Cape Air (9K) to Hyannis out of T5. They now use "gate 6A", which has its own podium and is actually the emergency exit adjacent to gate 6. You walk down the stairs to the ramp and are escorted (as a group) to your aircraft. At the time, there were two Cessnas at the "gate" - mine to HYA, and another to MVY leaving after us. We were called to board around 10 minutes prior to departure.
IIRC Cape Air used to be located towards the end of T5i (somewhere near gates 29 and 30, using a similar setup). I was glad to not have to walk that far. Annoyingly, however, the check-in desks are at the very southern end of the check-in hall, so if you're coming from the AirTrain as I was, it's quite a hike. At least PreCheck is at that end of security. The ticket counter was staffed with a uniformed JetBlue Airways agent as was the gate, as all ground operations for Cape Air at JFK are handled by JetBlue.
-J.