Loooong immigration line : JFK, BKK
Lack of food choices : LGA, ORD or pretty much every US airports I've been to.
Unnecessarily complicated, illogical layout : CDG (aka hell). FRA.
Come on people, why only dougnuts and fast food joints in US airports? Airport is THE place to make money on food. Everyone is locked up, for hours. Get a spa, get some bars and get some wifi connections.