Shirakawago/Kanazawa - These are two different towns but they are so close to each other and represent such different parts of Japan (plus most of the guidebooks don't really tell you who EASY it is to see them in the same trip) that you get a lot of bang for your buck.  Shirakawago has gassho zukkuri style of architecture and is a photographer's dream.  We went there in winter (which was wonderful) but were so envious to see what it looked like in spring and summer.  Just beautiful!  Kanazawa has some very cool sights as well -- a well preserved geisha district (it's not nearly as opulent as one would expect) and a samurai district.  Not to mention one of the best gardens in the country.  A large enough city that you've got lots of choices for shopping and restaurants, but small enough that you can easily see the sights in a few days.  In any case, for just a 2 1/2 hour train ride on limited express from Kyoto, this is a must see!!

Nakasendo Highway (Tsumago and Magome) - If you're not planning to go to Kyoto, you can more easily get to this piece of "Old Japan" from Tokyo.  These are two post towns connected by an old samurai "highway" where they have been largely untouched by the modern age.  The towns have been preserved in the original buildings and now hold small stores and traditional style inns.  Very cool and a great way to get away from it all.  

In any case, if you guys do make it down that way I can write more about logistics -- the trains are kind of complicated as you are a bit of the beaten path.  But in the mean time, I attached some photos to inspire you to get out there!  

OH!  And if you want a really good website for more alternative stuff to do...check this one out (he has a lot of interesting ideas for tokyo too).

http://www.quirkyjapan.or.tv/