Amsterdam, Prague, Budapest, Ljubljana, Venice, in January

Have you plotted the desired stops on a map, then calculated travel times and expenses?

Yes. Using Ryanair and staying in hostels it's very affordable!

You realize that you are going to be spending 30 to 40 hours on, or waiting for, trains and planes? If you figure 11 days x 16 waking hours a day, you will spend 20% to 25% of your waking time in transit.

I don't mind trains, they let you see the countryside! But if these are very boring rides with not much to see and you would reccomend something else please let me know!

Also we were thinking about taking the night trains when possible.

So, what about an itinerary that apart from Amsterdam, includes Ljubljana (one of my favorite cities) , Venice (another favorite city) and Rome? I'd fly the longer distances. Use Skyscanner and ITA websites to search various air connections and costs. Anyway, you asked for opinions.

Thanks Bruce I will look into Rome!

First of all you have to go to the places you really want to visit and don't compromise to much on that. BUT, before you make up your mind you really ought to consider concentrating on a tighter region so you spend more time doing great things and less time traveling. You have listed a half dozen really wonderful cities; but you missed the places in between. For instance (and I am not promoting anything here, just concentrating on something I know something about):
1 Fly to Prague
2, 3 Prague is a nice two full day visit (a full day is where you wake up and go to sleep in the same town)
4, 5 Prague to Cesky krumlov is a relatively short trip with some good scenery. Cesky K. is a good overnight town
6, 7 Cesky K to Vienna is another short trip and it brings you into another 2 full day city, 3 if you make a side trip to Melk.
8, 9 From Vienna you travel about 1.5 hours to Gyor and the Archabbey at Pannonhalma; and again, another good overnight stay.

10, 11, 12, Next an hour and a half away is Budapest. I tend to think its a good 3 full day town, but I am somewhat biased.

Got the idea. You are never in transit for more than a couple of hours and you see not only the cities but the wonderful towns and villages. The trip I just described is 12 days? You would need to cut either Cesky or Gyor from the trip. From Budapest fly back to Amsterdam (lots of direct flights). NOW, you can do something similar heading in any direction. You could fly to Italy and do a tour there or .....????????? Do lots of research. Look at all the inbetween places so that you have very little wasted time.

From Ljubljana or Lake Bled to Venice, a bus is more direct than the train connections (which often also include a leg by bus). See www.drd.si/en and www.goopti.com.

James thank you for your help. I agree that seeing some smaller towns and keeping it more compact might be a better idea!

After talking to my boyfriend we agreed that we wanted a more compact trip so we are now doing: Berlin, Prague, Vienna, and Budapest :)

I would tighten it up even more. Either do Amsterdam south to Prague or fly to Prague and do Prague to Budapest. You only hve 10 days.

James is right. You started with 4 destination cities, you still have 4, just different ones. It's not the extra hour or two on the train, it's the whole "changing cities" operation that takes up the time.