Tokyo area trains are running on a normal or near-normal basis.

The JR East Narita Express has resumed service, but they have not yet 
uploaded the revised timetable to their official Narita Express English 
language pages:

http://www.jreast.co.jp/e/nex/
It appears promoting the "Suica & N'Ex" package and trips to hot springs 
is higher priority: http://www.jreast.co.jp/e/index.html

Timetable in Japanese, from JR East:
http://www.jreast.co.jp/railway/pdf/nex_timetable.pdf

Departures from major stations posted here:
http://www46.atwiki.jp/earthquakeinfo_en/pages/40.html#id_1d9ac5dc
(Outbound runs from Yokohama, Shinjuku and Tokyo)

Rail services in Tokyo area, updated April 5:
http://www46.atwiki.jp/earthquakeinfo_en/pages/40.html

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Tohoku Line (local line) Kouriyama - Fukushima opens today.  22 runs 
each way.  Joban Line Katsuta - Hitachi - Takahagi and Mito Line will 
open April 7.