I went last year with a mate, we must have walked about 30 miles all over the city. Got up to the castle, checked a lot of the bridges out, got out of the city centre into the park. Found some market where knives and ninja stars seem to be the norm for your general stall
Tend to see lots of homeless people and beggers towards the parks and under the bridges which if you like your photography they can make some great 'real life' moments if you get me.
Lots of great bars around, tend to be a little more expensive in the new town.
Great erm..gentlemens club too haha (Hot Peppers). Sign on the door said no guns so leave that in the hotel.
http://www.timeout.com/prague/Appears to be quite a good site.