All wonderful places.
Krakow = one of the biggest (if not biggest) town square in Europe. It has a great atmosphere, especially at night and there's a pretty cool water feature. It's probably most inexpensive European city I've been to so make the most of it as. Be aware that you will be propositioned during the day, I mean morning and afternoon, by attractive ladies to come with them to a 'great club', the men are more upfront and simply say *the crude word for nipple* club? It goes without saying, avoid these people
Vienna = amazing city. It reminded me of London in a lot of respects, busy cosmopolitan city but with an abundance of beautiful and grand palaces. The scale of these places is ludicrous, I needed a wide angled lense to fit most of these palaces in. As you're only there for 3 days, pick and choose which museums / palaces you'd like to go in to, there's no way you can do all or even half. I personally enjoyed the photography aspect of the architecture so didn't go inside most of them. Take time out to go to Belvedere, it's a bit out there if I recall correctly, but there's train which goes directly to it. It is amazing with beautiful grounds.
There's also a theme park called Prater which has one of the oldest functioning ferris wheels in the world (1897 I believe). It's pretty cool to take some photographs of Vienna's skyline. I wouldn't go out of my way for it but if you're nearby I would definitely recommend.
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If you like nice cafes and cake definitely visit:
Prague = just walked lots and lots and lots, you can't get bored or run out of things to do. There's the old town across the bridge which has the Castle. It's a trek getting there if you walk but it's well worth it once you get to the top. The doughnutty cup things with ice cream called trdlnks are awesome (they are everywhere) definitely give them a go