Oh! My most favourite city; but then, I am from there!
The most commonly visited sites will be the Castle (and St. Vitus's Cathedral), the Astronomical clock, and the Municipal House. With the exceptionally cold weather we're having over in Eastern Europe make sure you bundle up for a trip up to the castle. You'll be going up and most of the sites you will want to see up there will be outdoors, or in drafty staircases promising the best view of the city. When going to the clock try to get there right before it is on the hour. Every hour on the hour, Jesus himself comes out.
Karlov Most is something everyone goes to see, so I would expect the bridge to be packed -- even this late in the season. It's a wonderful way to either walk to the castle or to cross into town to see the clock; either way, you will be given an excuse to cross no matter which side of the Vlatva you're staying on.
Absolutely go to Petrin Hill so you can get the most stunning view of the city. You should also visit Lennon wall to get a feel of the culture in Prague and the way the youth rebelled against the past and the city is continually moving forward. Try and cap off one day there with a trip to Globe Cafe, which is a real homey cafe.
Hope that helps! There are tonnes of museums to visit; the National Museum is stunning, or the National Opera, and they're all worth it. Have a spectacular time! about 5 years ago
There is also a free tour. With free, I mean that you take the tour (is offered in many languages) and then you give the guide whatever you want. The information is here: http://www.neweuropetours.eu/es/
Praha is a great city! I was there exactly one year ago, and I only can say that I love. So just enjoy! :) almost 3 years ago