All lines in the Tokyo area are open, but frequency is reduced to 80% of 
normal on most lines to save energy.  Due to changes in running patterns 
more transfers than usual will be required.  Even the Japanese are not 
sure what is going on.

If you have an appointment, set off early and devote some time studying 
the rainbow chart instead of jumping on the first train to come.  If in 
doubt, tell your destination to someone in uniform.  Show your ticket 
for it will give him a hint how far you are going.

Trains in the Tokyo area:
http://www46.atwiki.jp/earthquakeinfo_en/pages/40.html

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Rapid trains will start running on the Nambu Line.  The initial debut 
set for March 12 was postponed by the great quake.  This train stops at 
all stations north of Noborito and many stations south.  It never 
overtakes a local running ahead.  Don't worry unless your destination is 
a minor station, say Yakou.

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The strong earthquake of March 7 caused damage to roads and tracks in 
many locations in the Tohoku area.

The Tohoku Shinkansen north of Nasu-Shiobara is closed again.  Sendai 
area JR lines are also closed, but the Sendai city subway has resumed. 
A new round of inspections and repairs is on and re-opening dates of 
most sections have been set back.

The Tohoku Expressway suffered damage in southern Iwate.  Long-distance 
buses will be affected.  (Tokyo - Aomori, Tokyo - Morioka)

Transportation in the Tohoku area:
http://www46.atwiki.jp/earthquakeinfo_en/pages/15.html