Tokyo by a comfortable margin for me. Surely the most extensive mass transit network in the world and still manages to set the standards in terms of efficiency, timeliness etc. I really don't understand the complicated comments though, I find it very simple to use. When I first took my daughter to Japan she only took a day or two to understand things and from that point on she was in charge of buying tickets, getting us to the platform, directing us during transfers etc and handled it without a problem. She was 8 at the time.

I don't think anyone has said it's complicated to use. Just that it can be complicated to buy the right fare for.

Most visitors, once they get the hang of it, give up on figuring out how to buy the the correct fare completely. They just pay the cheapest ticket and use the fare adjustment machine at the other end and pay the difference there. Not all stations show you bilingual fare maps.

But if you change lines so that you leave one company's network and enter another's, even this tactic might not provide the most cost effective solution.

Perhaps it's because I was there for other reasons and not travelling as a tourist that I came across these difficulties - when I took my parents to Tokyo, they were also able to navigate the system and used it easily and successfully without any misshaps (partly because most of the main tourist sites can be visited using JR lines exclusively)

It's pretty easy to see if you are swapping between company lines though, every subway map sjows this clearly. If that's too much hassle then you can just get a t card and not think about it. I'd also argue that the fare adjustment machine makes things a lot easier than any other mass transit system bar those which have a flat fare.

Fwiw I'm often off in fairly far flung corners of tokyo, I can't think of any other city in the world where I could cover so much of a city without hiring a car

Another is the MRTA in Bangkok. Very new and very modern. Easy to use.

I have tried way too many subway/underground networks to rank them (probably 30-40 by now), but at least a few comments about some of them.

Paris: Very quick and efficient, when there are no strikes! You can go from Gare Montparnasse (southern Paris) to Gare du nord (northern Paris) in like 20 mins, which is pretty impressive.

Tokyo: Very quick, extensive network, and all info available in English. Very friendly station staff as well.
A bit confusing that there are two companies operating and not all tickets are valid on both, I don't really understand why this can't be sorted out.

New York: Not bad at all. I like to have the choice between either a slow train or an "Express train" when going to/from downtown Manhattan.

London: The world's oldest network, so quite understandably it's showing its age, but rush hour can be an absolute pain for anyone who is unfortunate to use it on a daily basis. Sometimes they have to close stations temporarily during rush hour as the platforms are too crowded.

Singapore: Super-efficient, Super-clean, Super-reliable, Super-punctual. Can anyone else think of anything to put super in front?

Stockholm: Works quite well and overall it's reliable. The trains run until 3 am on weekends which is a big plus and it's safe to use it during that time as well.

L.A: It's nice there is finally a subway in this city, hopefully it should reduce traffic a bit. Some of the stations are actually quite nice, like Hollywood Vine.

Metro in Washington, DC is carpeted. And the floor always looks grimy and dirty, overall very disgusting. It harks back to the start of the system when it was viewed more of a commuter rail from the suburbs than an actual big city subway system. Same reason why it has "train-like" seats, rather than rows of benches along the sides of the cars. So, if you have a window seat and it is your stop, you have to get the aisle passenger to standup and move out of the way. Time to redesign the cars.

I'm partial to Chicago because I've been riding it my whole life, but as others have said it has gotten to be a mess the past year or two. The blue line really isn't worth it from the airport to downtown these days with all the slow zones and what have you though hopefully the CTA will get that fixed sooner rather than later. The brown line seems fine to me during rush hour even with the service cuts and all that. During the day its not so great but cest-la-vie.

The new Francisco and Rockwell stations are both quite nice and I have similiar hopes for the new elevated stations. The renovated red line subway stations on State St are also nice. Hopefully they'll continue this trend.

My experience is that you can get pretty much anywhere on the L and maybe a bus after that, but that's just me having worked all over the city for a couple of years.

One thing I think the CTA in general has over many cities is the very simple pricing - it's a flat fee whereever you want to go plus an extra 25 cents to transfer. Most cities seem to have some sort of zone or time of day or other complicated mechanism. Chicago you put money on a card and that's it.

All that said Chicago's train network isn't the best by many standards. I love the DC Metro, the London tube goes everywhere although it seems antiquated in some ways. I'm in athens right now and their Metro while small is beautiful.

tokyo
 

Some people use the term complicated and confusing interchageably, if its confusing to smoeone they might just say its complicated. Because some find the fare system hard to figure out, in a way the fare system is complicated. Though not that complicated. Thanks to Suica, PASMO/Passnet and fare adjustment machines fare calculation can be hassle free.

For the purpose of tourism in central tokyo,
The average tourist doesn't ride a train that spans 3-4 different train companies through service on one ticket. They may ride one line before switching to one other line which may or maynot be for another company. To think the average tourist is traveling in Central Tokyo is not even riding the "subway" much unless for some spaces slightly outside the Yamanote Line or inside, I think most people try sticking to the JR Yamanote Line, I had a friend who didn't want to ride any other line @_@ . I don't have data to back that up, its just from observation.
There are many other train companies that operate in Tokyo but in Central Tokyo, its mainly JR or the two subway companies most travelers use.

Anyways in the end its not a debate, I find it easy to use and get around the city, thats what matters to me, I don't need to rent a car to drive around like for cities that have no public transit or trains at all. Trains connect to most sights people want to see in Tokyo when visiting.

-----
Washington, DC is nice and clean, goes to DCA which I like. It goes to downtown smithsonian etc, but georgetown isn't covered. Service to IAD would be nice when it opens (or ever opens lol). But I have a laundry list of problems with them.

I've been on many other systems, but Tokyo is my top pick.