For a budget conscious traveler, what is the best way to travel from Berlin to Prague to Vienna to Milan?

Have five days for trip and travel is to occur towards end of September 2006.

cant you take the train apparantley its not that expensive in europe

If your trip is only five days you really don't have much of a choice other than to fly. Unless you do over night trains but even those are going to land you spending some daytime on the trains. You should make the area you are traveling in closer together. If it were me I would just stay in Italy. I have been to all the places you are talking about and Italy is the one I would choose to go back to if I got a chance to go back to Europe. Also there is a travel company called DRI or DIR can't remeber but a travel agent should know (you can also look it up online and get info but only a travel agent can book threw it). This place has really cheep airfare to Europe and Cheap Eurorail passes. I was able to get business0 class airfare flying into Athens Greece and out of Madrid Spain, two nights in a 5 star hotel in Greece and a two month Eurorail pass for the cost of just my flight if I wouldn't have gone threw them. One last thing go to the book store and buy lonely planet for the areas you are going to they will also help you plan your trip and they are easy reading. Have fun Europe is Awesome!!!

As Berlin - Prague and Prague - Vienna are quite short distances you won't save much time by flying and also the night trains usually only run on longer distances.
So I agree with knockknock if you want to see Berlin, Prague, Vienna and Milan in 5 days, you won't be seeing much of each city but be on the road for a lot of the time.
I haven't been in Milan but I know the other three cities and each of these is well worth a five days stay alone.

Check out
www.lufthansa.com they have sometimes really great air fairs
If not then go by train.

Berlin is beautiful and the people were friendly. Seemed expensive, but food was reasonable.

Prague is also beautiful. Beware of pickpockets and car thiefs! The beer (as well as most merchandise) is very inexpensive, but coffee is about $6 US per cup!

Try the budget airlines--ryanair.com and easyjet.com.

I think this route is excellent by train. Flying is probably more expensive and certainly less flexible...maybe not even possible for such short routes. If you take trains in the mornings or even through the nights you won't loose much time travelling. Check out http://bahn.de for schedules. They normally have special offers Berlin - Prague (from 29 €: http://www.bahn.de/p/view/preise/surf_rail/surf_rail_internat.shtml). The rest of the trip shouldn't be very expensive neither.

A side note: don't let a medical issue blow your budget as well as your travel plans. With such a tight travel schedule, you run the risk of losing some money if you need to change arrangements at the last minute.
Go to http://www.wavehelp.com/trip-cancellation-insurance/index.htm and look at your options. You can get a free quote and even buy on-line if you wish.
Best wishes.