I went to Prague in 2011 when I was last in Geneva.
The first decision I made was to just fly there. Weekends away are too short to waste on travel time. I booked at the Novotel - it's called Wenceslas Square but don't be fooled, it's not actually in Wenceslas Square. It's fairly standard hotel, no real charm, but the price was good and it was clean. Everything is definitely in walking distance.
I used the Prague tourism site (http://www.praguewelcome.cz/en/) before I arrived. One of the good things on there are suggested itineraries for 1, 2 or 3 days which at least make sure you take in the main sites.
When I got to the airport, I just took the normal public bus in to the main train station. You buy the tickets in the arrivals hall at the airport, they are much cheaper than any other alternative and you get to see Prague's suburbs on the way in.
I love walking, so I didn't use any other transport options really - but I did take a ride on their metro just to see what it was like!
I'll let you explore the tourism websites for information about sites. My only real tip is to hang around the Old Town Sqaure on the Saturday night. When I was there, there was some sort of festival on - lots of food and wine stalls, a stage with free concerts and even some pole dancers!
My photos from Prague are here: http://www.flickr.com/photos/anura/tags/prague/show/
Jul 5, 13 10:20