I've been to a ton of these places.. A few of my favorites:
Nico's Pier 38 in Honolulu
Lankford Grocery in Houston
Mike's City Diner in Boston
Red Arrow in Manchester is overrated IMO. Good place to spot politicians though!
I don't remember the name, but I went to the place in Omaha in the old school cafeteria. Meh.
I've never been too any that are absolutely horrible though.