I have to agree with everyone that for point to point travel in general the train is the best option in europe. And definitely get a first class eurail pass. Not on the german rail system, but definitely in other countries (france, spain, belgium) and some select trains (TGV THALYS) you will have to pay a booking fee.
last October, me and family (5) flew to FRA and did a round europe train trip, Paris, bordeaux, madrid, Barcelona, Nice, Rome, Salzburg - FRA.
Booking fee ranged from about $15 to $45. The $45 was only on the Spanish trains and that included a full meal service with drinks cart. (much better than QF Y service)
I fully researched this trip for 12+ months before hand using
www.db.de the swiss (CFF) train website was also very useful along with the french (SNCF) and spanish (RENFE).
This time however with family in tow and knowing exactly which days we were travelling, I am questioning the Eurorail pass value, and I believe I may have been able to save money doing advance bookings (with the Terms & Conditions risks). Definitely check before hand.
I could not beat the value of the eurail pass at all. Even with the extra booking fees the price was still significantly less, than getting individual fares.
We also got a eurail pass for our 3 year old, who could technically travel for free but only sitting on a lap. This was a great saver, in particular, on one overcrowded 2nd class regional french train as we put all our luggage into the kids seat, instead it being out of sight.
Going over the dolomites is a great trip on the train.
FRA to PARIS was good. went via Karlsruhe, had a great afternoon there. The other way is via belgium, which is quicker but adds another country to the rail pass.
Night Trains are a good idea. Pros: you save on a hotel room for a night, light breakfast included.
Cons: The booking fee is quite high, don't see the scenery, trips can take a lot longer than in the day, No shower for over 24 hours