This company offers balloon trips for the cheapest I've seen (but I haven't looked too hard). Trips are about 5200 CZK per person (a little over 200 Euro) but these are also outside the city.
They also offer another product, called "upoutany balon" that is in the center of Prague. This one only costs 800 CZK per person (about 35 Euro, more or less) and takes two people up in a small balloon right in the center of Prague. This looks fantastic, and I think this would be a great thing to do. On the website you can see the pictures, and there are also a bunch posted on Flickr from people that have done it.
Hope this helps! If you have any other questions, just let me know. Ray