A few beautiful but smaller places for the sake of variety:
Sopron and Gyor in Hungary. Both less than 80 minutes from Vienna by train. Gyor seemed to have a larger historic district, plus several small art museums. Sopron you might be able to see pretty comprehensively if you had an afternoon and evening free.
Olomouc, Czechia. Very pretty, historic, university town. Not overrun by tourists like Prague. I see a morning rail connection that takes just 2 hr. 19 min.
It appears that both Zagreb and Ljubljana are awkwardly long train rides from Vienna. Buses might be a bit faster, but of course you never know what traffic will do to a bus schedule. Those two capitals are about 2 to 2.5 hour apart, so if you have a really long weekend it might be tempting to try to see them both on one trip. Do not miss the Museum of Broken Relationships in Zagreb.
I find the Deutsche Bahn website the easiest to use for checking most European train schedules, but you'll need to use others when you want to see fares and buy tickets. The Seat61.com website has voluminous information about European trains and will point you in the right direction for ticket purchases.
For bus trips and combination rail/bus trips (or even air/train or air/bus trips), it is sometimes useful to start with Rome2Rio.com. However, you must understand the limitations of that website: You simply cannot trust the specific fares, travel times or frequencies it displays; they are often wildly inaccurate. What the site is good for is identifying the transportation companies (especially bus companies) providing the service you're interested in. Just keep drilling down and you'll find the company names, and usually also links to their websites.
Although buses and local trains (those stopping at a bunch of small towns) are often exceptions, you will probably find wide variation in fares, depending on how early you buy your tickets. It can make a very large difference, last-minute fares sometimes being double, triple or more the amount you pay if you are willing to commit to a non-refundable/non-changeable ticket purchased super-early. And the budget-airline tickets follow a similar pattern. So it's very much worth your while to plan ahead for the longer rail trips and all the flights you want to take. Just one example: Buying a one-way rain ticket today to go from Vienna to Munich would cost you about 30 euros if you wanted to travel on January 7, 70-80 euros for tomorrow or over 100 euros for today.
