Assuming that you you plan trip Vienna-C.Krumlov/Prague-Warsaw the best options for you are - purchase in advance discounted Spar ticket from Vienna to Prague on the OEBB website (link you will find here -
http://europetrainsguide.com/200907166/Countries/Austria/Austria-OEBB.html), it will cost you 29 euro.
From Prague take either train (248CZK one way or 447 return - valid two days) or bus to C.Krumlov. Come back to Prague and purchase one way Prague-Warsaw ticket - 42.4 euro
Other option is to go directly from Vienna to C.Krumlov - if you are traveling alone it makes sense to look at EURegio ticket Wien-C.Budejovice (22 euro), from C.Budejovice just take a short train ride to C.Krumlov, afterward Prague etc.
If there are at least two of you than it worth looking at Einfach-Raus-Ticket (28 euro) till last Austrian station Gmund NO, afterward just purchase Czech domestic ticket on board of a train C.Velenice-C.Krumlov - 189 CZK
In case you want to come back to Vienna after visiting Warsaw, than probably it will be cheaper not to purchase one way Prague-Warsaw, but to buy Bohumin-Warsaw-Bohumin (34 euro)+ domestic ticket Prague-Bohumin(445CZK) and while in Prague domestic ticket from Bohumin to Breclav (239 CZK) + Brno-Vienna ticket for 9 euro for you return journey from Warsaw to Vienna.
For all the timetables in order to plan exact route, train changes etc. see -
http://reiseauskunft.bahn.de/Good luck
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