Any domestic airport that requires gate-to-gate security - JFK and MIA (at least in the past), and SAN for the commuter terminal.
Endless concourses with no moving sidewalks - ATL comes to mind.
HNL wins the prize for confusing check-in, and the walk from International arrivals to UA can be brutal.
Idiot CBP practices, like deciding to merge foreigners and citizens, where the foreigners have to be fingerprinted, photographed, and interviewed.
Signage, signage, signage.