All lines in Tokyo, Kanagawa and most lines in Saitama, Chiba will be 
open today.

JR Joban Line opened to Mito and Katsuta.  JR Ryoumou Line is also fully 
open.  It seems that the "Hitachi" limited express services are not 
running yet.

Seibu, Tobu and Tokyo Metro have announced timetable changes for April.
Through runs between Seibu, Tobu and subway will be restored.  Tobu will 
restore limited express services to some extent.  Seibu will run limited 
express trains on weekends.

Details here:
http://www46.atwiki.jp/earthquakeinfo_en/pages/40.html
(Note that the page has changed.)