...
Conclusion It is not the site RIKEN that has gone bad, rather it is some of the routes
RIKEN Looking at Japan
Japanese hosts seen from JP.RIKEN.N3 (RIKEN) see no impact on RTT
It looks the problem is in the route to Japan not within Japan itself. I wonder if the undersea earthquake has disrupted some cables? This appears to be in line with the information from [from http://www.renesys.com/blog/2011/03/japan-quake.shtm|http://www.renesys.com/blog/2011/03/japan-quake.shtml]
Routes
Comparing the routes from SLAC to RIKEN (ping.riken.jp) and from SLAC to NET.APAN.N2 (ns.jp.apan.net) we see RIKEN has more hops and goes Eastwards via the Avenue of the Americas in NY, while APAN goes directly via Sunnyvale near SLAC and then via Pacific Wave directly to Japan. The traceroutes from SLAC to the University of OSAKA and the University of TOKYO are similar to traceroute from SLAC to RIKEN.