Interactive geographic Tokyo train/subway map
 

I've been looking for something like this for a couple of years now, stumbled onto this while looking for something else entirely:

http://japonyol.net/editor/railway.html

I can't vouch for accuracy, but it seems to be pretty good for what I've looked at so far. I do note that it only shows NEX to Tokyo and not the other branches. Also, you can only view one line at a time - the option to view all subway lines leads to a 404 error.

While schematic maps are great, this will show you where the lines run geographically.

Cool! Good find.

You could just fire up Google Maps and choose the "Transit" option to see all subway lines at once.

interesting! There are a few additional tools from the same web site.

This page let you search all the train stations within 1km from a spot you choose (by centering the map).
http://japonyol.net/editor/radius.html

This is the Japanese version of the map, but has a more convenient interface.
http://japonyol.net/editor/ajax.html

All Subway Lines works now. It's pretty neat. :D

Yeah, I found that out yesterday and you beat me to the punch...

It would seem that someone is actively working on this, but I can't read Japanese (is the other language Spanish?) so I'm unable to figure out what's going on.

I'd love to send some input to the author but I can't figure out how.

http://japonyol.net/editor/comment.php

Or the email address on this page
http://japonyol.net/editor/about.html

Well, it's updated with more functionality and some new maps...

However - the maps provided are now in a fairly small rectangle, which unfortunately tends to wreck the whole thing for me. :(