I have a friend who's ridden every rail transit system in the US. He made a spreadsheet to act as a checklist. I copied it and now track my own progress. You can see my checklist
here. I've ridden or at least been to a station and seen a train for 48 of the 87 metro, light rail, commuter rail, and streetcar systems in the US.
Outside the US, add another 8 from Canada and another 6 from Europe.
Paris is my favorite by far. If I have to stick within the US and I avoid the homer answer of WMATA, I guess I'd say I have a soft spot for SF Muni, because I want every city to have an urban light rail system.