I've been having troubles finding a good way to buy a train ticket from Prague to Vienna. It seems I can on this website but I've never heard of it before or had someone recommend it so I'm wondering if anyone has used it before.
Sounds like RailEurope east. They offer €40 tickets from Prague to Berlin. You can get a Europa-Spezial ticket from Prague to Berlin from the German Rail website for €29.
THIS site is the official Czech Rail link from which to buy tickets. However, I just looked up routes between Prague and Vienna on August 11th (saw the date in your other post) and several of the routes gave me the message "The requested ticket is no longer available." I think this means that the discounted 19E fare is sold out, but not the actual train. The EC79 Gustav Klimt train still seems to be available at a discount (500KC, or about 19E), it leaves Prague at 14:39 and arrives Vienna at 19:29.
I believe these discounted tickets go on sale 60 days in advance and the good rates may have sold out.
If traveling on a budget is a priority, and because in your other post you asked about buses, I just wanted to chime in to say that I've taken both Student Agency Bus (day trip between Prague and Plzen) and Orangeways (from Budapest to Vienna; don't think Orangeways operates out of Prague, though) and would do it again in a heartbeat. For us it was very comfortable, they each offered complimentary coffee drinks and headphones with which to watch movies/TV shows, and the bus stewards were multi-lingual and friendly. The only caution I would add is if you are tall (over 6'2", maybe?) then the seating might be less comfortable than the train.
Lastly (I promise!), I like the following site for sussing out travel in/around the Czech Republic, it gives you the option of seeing both train and bus options at once:
www.idos.cz (make sure it's .cz, .com will bring you to the Int'l Dutch Oven Society. I couldn't even make that up).
Good luck!