Originally Posted by railroadtycoon
A bit on going to Nikko from Tokyo.
JR has a direct train from Shinjuku Station to Nikko, however this train is in joint service with Tobu Railways, so if you use a JR Pass on this direct train you will have to pay a supplimental fee (1000+ yen or so? not too sure) for the Tobu Railway portion of the trip.
Otherwise, for the "free" way take the Tohoku Shinkansen to Utsunomiya Station, then change to a local JR Line to JR Nikko Station.
There aren't very many of these trains, and I bet the supplement is closer to Y2,000 -- each way. From Shinjuku, with a JR pass, take a Saikyo line express to Omiya and switch to a shinkansen to Utsunomiya, then follow as above. It is worthwhile to check out the local JR line schedule to Nikko in advance to avoid up to an hour layover in Utsunomiya. That JR local line is really slow, but when combined with the shinkansen, total time to Nikko is about the same as a Tobu line limited express.