I'm planning a large trip in Europe. What would the best program be to help me plan?

You can try http://tripfeet.com. It's focused only on Europe and integrates train data with flight data. However, it is still in beta.

When planning a trip, I use tripline to make a 'wish list' of places to see in the areas I am going. I then prioritize them and make a rough plan. I then get to my destination, chuck my plan out the window and go where my heart, interests and the people I meet along the way lead me. :-) I am currently in the last weeks of a 4-month trip to Europe/north Africa. Before I left I booked 4 internal flights to move me around during my trip. I have used 0 of them. Of the 10 countries I had originally planned to visit, I will visit 6 of them as well as an additional 2 I didn't plan on seeing.  I wasted a chunk of money doing too much advance planning and I am glad my trip has turned out the way it has instead of the way I planned it. So, to make a long story short, plan for your trip, but don't tie yourself to those plans so tightly that you can't change them if a new/better opportunity comes along.

I can't suggest the order but the cities that must be visited I can say : London, England Glasgow, Scotland Reykjavik , Iceland Ibiza , Spain Barcelona , Spain Madrid , Spain Lyon , France Paris , France Cannes, France Marseille, France Alps, France& Germany Munich, Germany Berlin , Germany Dortmund , Germany Vienna, Austria Zurich, Switzerland Brussels, Belgium Prague, Czech Republic Milan , Italy Sicily, Italy Rome, Italy Amsterdam , Netherlands The Hague, Netherlands Oslo, Norway Copenhagen , Denmark Moscow, Russia St. Petersburg , Russia Constantinople , Turkey I know all cities are not possible, so I'd say choose from these to maximise your trip and exposure of Europe.Hope the answer helped