Last fall we stayed at the Ibis Mariahilf in Vienna and enjoyed it very much. Important to ask for a back room however, as those facing the street are impossibly noisy. The Ibis Mariahilf has almost all European clientele, is budget but newish and very clean, modern elevators, and even some semblance of air conditioning, though not very effective. (Yes, we needed it.) Blond furniture, good buffet breakfasts.
In Prague we have stayed at the Esplanade, at the Hilton Atrium, and at the Marriott. Of those three, we enjoyed only the Hilton Atrium. The Marriott was just too formal and cheerless. No one ever smiled. The HIlton is out of the way, unfortunately, and when we were there, our room was a garish pink. Still, it was a far happier experience than the Marriott. YMMV.
I agree with the other FTers that taking a train is a better choice than driving. A lot easier, assuming you buy your rail passes beforehand.