You have big stations and then smaller stations.
I've used the following larger Stations (which I include since they generally serve multiple trains a day and are in a big city):
Boston
New York
Philadelphia
Washington
Chicago
New Orleans
San Antonio
Los Angeles
Seattle
Portland
I've used the following smaller stations:
Whitefish, MT
Pasco, WA
Orlando, FL
Lakeland, FL
Kingston, RI
Providence, RI
Portland, ME
Poughkeepsie, NY
Trenton, NJ
I would say my favorite big-city station is actually Boston. It has a great lounge, nearly everything in the station is on one level, it's easy to navigate and offers high-level boarding on every track (my biggest qualm with Washington DC and Chicago).
My favorite small station is Whitefish, MT since it is very pretty, offers a car rental desk right in the station that's easy to get to and is very charming. I get similar vibes at Lakeland, FL and Kingston, RI, both which offer easy boarding and local charm at their stations.