Prague to Vienna

Just take the regular RailJet train for the fastest connection. There is a different route via local trains available, more scenic, but one hour longer.

I have not done Sidetrip Tours, but (1) I have used a company called Daytrip to drive me from one place to another with stops along the way and (2) I have used a local company in Bosnia & Herzegovina to make some stops with a transfer from Mostar to Dubrovnik. I looked at Sidetrip's website, and it looks like they have a couple of good options depending on your interests. So... while I can't say that I know Sidetrip, I can say that I am a fan of the concept of adding interesting stops along the way when my schedule allows it.

Like Dave, I've used DayTrip too, a few times. They did fine and I presume SideTrip will do good too. I think its always better, when time permits, to slow down and see the world between the tourist attractions.