hostelworld.com is the site that I've used when backpacking in Europe. Lots of options there for all different levels of lodging.
Some of these countries, when you get in to the beach towns, there will be little old bubushka ladies at the train station offering cheap (usually REALLY cheap) accommodations. Again it depends on what level of comfort to cost you are looking for.
If you're going to stay south, Vienna is a cultural capital, kind of like an eastern Paris. Haven't been to Budapest but I hear very good things.
I personally like the weirder countries in Europe with less tourists. My favorite place in Eastern Europe was Ukraine and if I were going to the region that you are, I'd probably go to Hungary Serbia, Albania, Croatia. Albania hasn't made it in to the EU yet and the stories I've heard from people who went through there were pretty entertaining. Then again, my idea of a good time is drinking with shepherds and the like.
Romania had the prettiest girls that I saw in Europe and I heard that Croatia is up there too. And in the summer, parts of Croatia become huge havens for Russian tourists. (Who know how to fucking party!

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