I haven't been on a lot of transit systems in the country, so I really can't decide on which one is my favorite. So, I want to hear what your favorite transit systems are.
SF MUNI and everything else over there, hands down.
Going based what I've ridden, MBTA for its variety of modes, MTA in New York for depth of service, and the DC area TA's for interfacing and variety of equipment.
Going beyond that, I'll second Tristan's vote for the Bay Area TA's and toss in votes for the Seattle area TA's and the TTC.