If you want to know if it's worth helping through a 'known' registered charity, check and see if they have a Human Resources department. If they do don't touch them!
What I found - after volunteering myself vehicles and time was that 'administration costs' would take a huge chunk of anything going.
Just to reinforce how well Japan is doing in picking itself up, I seen a story this morning regarding a major road that was devastated (actually looked like ours here in normal circumstances) and they had it in brilliant condition within days (like we would like to have ours).
They have had a devastating period, but they have had wonderful periods that allow them to pick it up again, and the people don't shirk it.
By all means wallow in sorrow for them, but do feel deeply regretful at the loss of life, and leave them to sort it out - they are way more than capable and all the intervention is just going to make things take longer as they try and organise all the bloody well wishers with a pair of socks in hand trying to help - wonder what the Japanese is for bugger off were doing fine now!