casper - i got lots of help from this forum "virtualtourist.com" check it out! Lots of links & tips, including rail, travelling between places, things to see etc.
If U havent book yr air tix, I would suggest U do
Prague first as Vienna is in the middle.
Prague - (can do day-trip to Brno on way to Budapest) - Vienna - Salzburg - Switzerland.
At Salzburg, U can also do day trip to Munich
From Vienna, U can do day trip to Bratislava (Slovakia).
As for rail tix, U need to calculate if its worthwhile. Since U travelling into Switzerland, the Europe East pass doesnt work in Switzerland. You can either get Europe East pass, and then a separate tix for Switzerland. Or another type of rail pass that allows U to mix & match the countries youre travelling.