I'm surprised that no one has mentioned Penn Station, New York in this category. What a dump that place is, and has been for as long as I can remember (and, yes, that includes the original Pennsylvania Station).
NYP is a haphazardly arranged maze that is crowded, filthy, and even dangerous. It's had more unsuccessful facelifts than Joan Rivers. There are few places to sit, and if you find a seat, you will in short order be solicited by one or more of the local "characters" that inhabit the facility. Food options are basic, and most are not in the Amtrak portion of the station. Need to use the facilities? Oh boy, are you in for a treat. I shudder to think of the female perspective of that issue.
I have not been in any train station or airport in the world worse than Penn Station, New York. If someone has to frequent NYP on a regular basis, AGR Select+ with its Club Acela access would be worth its weight in gold.