Most railway lines are back to normal rush hour schedule today.  An 
important exception is the JR East Joban Line, which is terribly crowded 
due to low frequency.  During daytime hours runs will be omitted on 
almost all lines to save energy.

Shonan Shinjuku Line services resume today.

JR East Narita Express is running again, but there is a wide blank 
during mid-day.  Furthermore, the official Narita Express web pages have 
not been updated:

http://www.jreast.co.jp/e/nex/
(As of this writing, it says that Narita Express is "still suspended")

Here is the timetable in Japanese, from JR East:
http://www.jreast.co.jp/pdf/untenkeikaku.pdf (3rd and last page)

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

Keisei Skyliner schedules also change from today:
http://www.keisei.co.jp/keisei/tetudou/skyliner/us/index.html

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Rail services in Tokyo area, updated April 4:
http://www46.atwiki.jp/earthquakeinfo_en/pages/40.html