Since my list is a personal selection, it follows my predilections. Since I didn't state these earlier, here they are now:
1. Subway should be a short walk.
2. Immediate surroundings should be at least interesting, if not lively.
3. Hotel itself should make you feel you're glad to be there. This means a friendly staff, clean rooms, nice public spaces, responsive service.
4. The place should represent some perceptible event or stage in the city's history or evolution.
For example: Copley Plaza speaks of Beaux-Arts opulence; Inn at Harvard speaks of Graham Gund's post-Modernist playfulness; Custom House is the transformation of once-important government offices; other inns are converted townhouses and allow you at least the illusion of being a resident.
In other words, the facility itself is part of the visitor's experience and illuminates the City's history and essence. This means there's not much value to a purpose-built Hilton or Holiday Inn; when you stay in one of those, you could be anywhere.