The Vienna to Prague train is ok. It's short on amenitities and 4.5 hours long. They still use the individual cabins instead of the airplane seating style. The day we took it (a Wednesday afternoon in May), we had a cabin of six seats to ourselves.

The only thing is that when you get to Prague, you're not at the main train station. You're at an outlier station in the NE corner of town, and you have to take the subway line into the heart of the city. If you use the ATM machine, make sure you don't take out an even big multiple of currency, or you'll be like me trying to figure out how to break a 1000 kr. bill for a 12 kr. ride.....