PPS (Prazska praoplavebni spolecnost) is major provider of boat & river cruise service. They run boats on the River Vltava during the summer months. Most frequent boats run to Troja, which is a northern Prague suburb. There are also river cruises around Prague from April to October (and limited cruises during winter) with food and drinks provided (cost around from 200CZK to 1000CZK). Besides PPS you can find some other small boats companies running their boats in summer. It is always good idea to book river cruise in advance as there are limited seats available.
 
Specail offer: Dinner on the River including tour guide

For younger people and teenagers, but not limited to, there are summer parties and disco boats operated by one or two radio stations. They’re popular in summer with live DJ shows. Entry free is around 100CZK. Journey take around 4 to 5 hours starting around 19:00 and finishing around midnight.

A bit of good advice. Everyone tells you not to trust the Czech taxi drivers especially to and from the Airport. Simple solution book and prepay your taxis through Prague-Airport-Transfers (they are on the web) It was less than £30 return and the service was superb. England, DEC 07 source TripAdvisor.com Most UK customers recommend Prague Airport Transfers.

If you are looking for some unusual Prague sightseeing, you can take advantage of Prague Venice boat trips and see Prague’s main sights from the perspective of the fisherman sailing Vltava river with his boat 100 years ago. You will be taken to places which are not so often visited by tourists, for example: watery casemates of the Old Town, Certovka channel and many others. From the boarding place at the site of the former Judith Bridge (by Krizovnicke namesti) you will be taken through a lagoon under Karlovy Lazne (Karlovy Spa) and then you will admire magnificent views or Prague – Prague Castle, Petrin Hill, Lesser Town roofs,. National Theatre and then a drive under the Charles Bridge and continues to the Certovka channel. You will be introduced all places seen within the boat drive, all important historical events relating to route by professional guides speaking English, German, Italian, Spanish and franc. Wooden Prague Venice boats are unique, as the were built as a copy of original boats sailing Vltava at the end of 19th century. They have flat-bottomed craft sited high up in the river enabling to enter Certovka channel, other tunnels and narrow spaces.
You can enjoy this pleasant experience either in summer as well as in winter, as all boats are heated and roofed. Cold drinks are offered in summer, boiled wine or hot tea provided in winter.