My worries about Japan aren't about the radiation (which might be dangerous if you spent months or years there but certainly won't be a problem for short stays). My worries are that it is probable that the general area will receive a huge 7.5-to-8.5 magnitude aftershock. There's evidence that the stress on the fault is stronger south of the 9.0 quake's epicentre than north, and that puts it fairly near Tokyo.

Of course, this quake could hit next week, or next month, or next year, or five years from now. Or not at all.

Connecting through Tokyo is probably perfectly safe, but the rational part of me is delaying any planned Japanese vacation for at least four or five years until the worst of the fault instability has settled down.

Sumatra (9.1-9.3 in '04) had an 8.7 aftershock in spring 2005. I don't expect a Japanese aftershock to be that large, but something in the 8s is possible.

The joys of seismicity!