1. The Washington DC Metropolitan Transportation Authority (or METRO for short) - Convenient, no echoes (they have sound absorbing pads on the walls and roof!), and it's easy to navigate i.e. no huge crowds very often. Plus buses are no more than a block away!
2. My very own RTD, also known as Denver's Regional Transportation District - I use it, nothing is more than 5 mins late (usually...) and they are expanding their light rail... the bridge over 6th avenue at union street is a little unconventional for Denver but it's nice to see some change
3. My third would be the NYC Subway because of it's influence over subway development in our world... unless there was a subway before that?