Trouble connecting the dots...

Amsterdam and Brussels are a long trip each way from Prague/Munich. You could fly, but I'd personally put them between London and Paris on your itinerary.

Prague>Amsterdam>Munich available via City Night Line trains. Single sleeper cabins are available now at reasonable prices.

Your itinerary is busy. Personally I'd cut 3 destinations and spread those days among others. But it is not yet an insanely "looks like a work schedule of a travelling salesperson", so it is 'doable'. I'd look from a flight from Sevilla or Malaga to Switzerland and spend at least 4 nights there. Granada and Zürich are as far apart as Los Angeles and Denver, it is not a feasible distance to travel by train at all. I would also change the itinerary after your Bologna stay. I'd fly to Amsterdam, then: train to Bruxelles, day fly to Wien, then train to Praha, then train to München. If you decide not to visit Amsterdam and Bruxelles, you can visit Berlin and then make something like: from Bologna fly to Wien then train to Praha, then train to Berlin, then train to München. Yet another alternative is that, if you are willing to cut down the cities, you do like this: - London, fly to Amsterdam OR Bruxelles, train to Paris etc. etc...., then fly from Granada to Bologna (or any nearby airport combination like Malaga/Malpensa + train)
- from Bologna, you train to the Swiss Alps, then fly to Wien, then train to München.

One small specific suggestion, which is to go Bilbao > Madrid > Granada > Seville, then fly out of Seville, if you can get a good flight. You'll avoid doubling back. If you can fly out of Granada (it's a small airport so I don't know), you can go Mad > Sev > Gran, which would be even better. Flying from Bilbao to Granada would make Gran > Sev > Mad possible, also good though I do not know how feasible that is. You do not include travel time in this itinerary, which makes me wonder if you have really thought about what it will be like to spend so much time getting from place to place, and to change venues so frequently. Many of these are day-long connections. My philosophy is that is a place is hard to visita day to get to and a day to get from, sayI won't go unless I have time to do it justice. Otherwise, exhaustion and frustration. That's a personal choice of course. Have a great trip.

Thanks for the suggestions so far. I know some of the travel days will be long but all my stops are art history graduate must-sees and worth the time for me -not just going for the Facebook pic, thank you very much :) The flight search has been pretty unsuccessful but I think I found something that will work. Bilbao-Madrid-Seville (cut the night in Granada, day trip instead) fly to Milan, train to Bologna train to Switzerland-fly to Vienna from Zurich-train to Prague-then into Germany
The only thing I'm concerned about with these flights is getting to and from the airport and luggage restrictions. It seems that as long as you add a checked piece when booking online it doesn't end up costing too much. I'm saving Amsterdam and Brussels for another time so what cities need an extra day, probably Paris, Madrid, Alps?

Hey Melissa, I'd suggest London to Paris on the Eurostar given time constraints and it travels from central London to Central Paris in a little over 2 hours. There is a one hour time change.. France is 1 hour ahead. No point dealing with airport lines and flights. Buy your tickets as soon as you can to get lower fares: http://www.eurostar.com. NOW would be a good time :) Paris to Bordeaux... The train takes about 3 hours... http://www.sncf.com/en Bordeaux to Bilbao a little over 4 hours on the bus. Checkout the "favorite links" tab for bus schedules. You can do the Mardid-Seville-Granada-Madrid triangle on the train and NOTE that the AVE (the Spanish high speed train) operates between Madrid and Seville. "Renfe" is the Spanish rail network: http://www.renfe.com/EN choose "AVE" where you see it on the booking schedule. You can buy the train tickets in advance. You didn't say where in Switzerland you want to fly to... Anyway you can fly Madrid to Geneva on easyJet, daily departures.. http://www.easyjet.com/en. Take the train to your Alpine destination. Then Switzerland to Bologna.... train probably depending on where you are. Ryanair flies from Bologna to Brussels http://www.ryanair.com/en and easyJet flies from Amsterdam to Prague..
Note also that RyanAir only allows 15kg while easyJet is 20kg.

Depending on what you want to see in Munich (don't know what your interests are), you could add a day to the Munich area if you want to head south to see the castles. In your most recent post, you mention flying from Zurich to Vienna. You could take the train and stop for a night, or two, in Salzburg on the way to Vienna. Salzburg is a small, compact city and is just beautiful. It's really worth a stop. Have a great trip!

I believe there is a direct bus route from Bordeaux to Bilbao. I can't bring myself to cut it out as I really want to see the Guggenheim. The Seville-Milan flight is through RyanAir or Vueling. If I stick with flying Zurich-Vienna it would be through AirBerlin. When you book these discount flights, are all the fees and surcharges included, or do they add charges when you get to the airport? I'm thinking the Swiss part of the trip will work the best after Italy. That way I can stop by the Matterhorn on my way into the Bernese Oberland. Salzburg is a great suggestion, I don't know why I hadn't thought of it before, love Baroque art and music! I will buy the Eurostar ticket hopefully tomorrow. Trying to decide if I should do 4 or 5 nights in London. Thanks again for all the thoughtful advice!

Your question "When you book these discount flights, are all the fees and surcharges included, or do they add charges when you get to the airport?" All the fees and surcharges are paid when you purchase your ticket online. However, these airlines, especially RyanAir, WILL charge for excess weight over luggage allowance. And it can a significant amount, check out the costs on the respective airlines' websites. If you are carrying more than the allotted amounts, pay for the excess bags at the time of booking.

And adding to John's comment on Ryanair, they have even more unusual fees than just the luggage fees. For example, you need to print your boarding pass before you arrive at the airport. If you get to the airport and don't have one, they will charge you a fee of 60 EUR to print the boarding pass. Even with the luggage fees, Ryanair charges one price if you pay the fee when you book your ticket and a huge fee if you wait until you get to the airport. They do list all their rules and fees on their website. If you plan to use them, you need to study them.