Where to go between Tokyo and Takayama?

Looking for an interesting place for 1 night after 3 nights in Tokyo and before we head to Takayama for 2 nights (then 4 in Kyoto, 1 in Koyasan and then back to Tokyo for our last night. Hakone caught our interest-maybe Kanazawa. An onsens in Gifu but which one? Is there something on the way--we will be traveling by train. We're buying a pass-another ?-Can you pay an up-charge to ride on the Nozomi with a pass? Thanks.

Between Tokyo and Takayama, I vote for Matsumoto. You can get there by train but then you have to go on by bus to Takayama - but it's not expensive and it's a beautiful trip.
Matsumoto has a real, non-reconstructed castle. If the weather is clear, you can see the mountains all around. There are some nice shopping streets and it's just a pleasant place to spend some time. Just outside town, and very accessible by bus, are two onsen areas: Utskushigahara and Asama.

no you cannot upgrade your JR PASS to use the Nozomi. Nozomi refers to the fastest Shinkansen, not to a special looking train. Some Nozomi are very beautiful, other just plain and don't look any different than some of the Hikari that you will use with your JR pass. I second a side trip to Matsumoto. use the "Sneaker" a cheap bus that goes around town in a loop. it starts/ends by the JR station

Definitely Matsumoto Castle. It is within walking distance from the station. about 15mins. Beautiful especially during spring when the castle is surrounded by sakura and you can see the mountain range fr the castle.