[electricron]

Originally Posted by Wizened Variations

Multiple loops feed on each other, particularly if each loop intersects the other at more than 1 station. Two or four would be better.

Here are links to successful systems with loops that are highlighted. Granted these are huge systems but the principal works the same. These maps are idealized for visualization not geographic accuracy.

London
http://speedymole.com/Tubes/London/l...-tube-map.html

Moscow
http://speedymole.com/Tubes/Moscow/m...map-metro.html

Seoul
http://wallpoppy.blogspot.com/2011/04/colourblind.html

London, Moscow, and Seoul have rivers bisecting them less than a mile wide. The Bay Area has San Francisco Bay bisecting it, which can be 4 (Bay Bridge) to 7 (San Mateo Bridge) miles wide and 33 miles long (Bay Bridge to Milpitas). Putting those distances into prospective, 33 miles in the London area stretches from M25 west of the city to M25 east of the city as a bird flies along the Thames. The English Channel between Dover and Calais is just 25 miles wide. Yes, just the south Bay is longer than the crossing.
The Bay stretches further north, and just by itself (uninhabitable swamp and bay) is larger in area than central London.
I don't think the Bay Area is geographically the same as the three cities you mentioned, and I highly doubt circular transit patterns will work. The Bay Area is set up for linear transit lines, not just by the Bay coastline but by the surrounding hills/mountains as well.
Ignore the landscape and distances involved at your peril. I don't think you would advocate building a circular tunnel under the channel, so why are you suggesting building a circular transit lines around the south Bay?