If your kids get tired of sightseeing, you can always take them to the movies. There are a number of large multiplexes in the Prague city center or close enough to it and they usually feature some films suited for children. There is also an IMAX theatre in Prague. Here is a list of some movie theatres that are easy to get to:

Palace Cinemas at the Slovanský dům (Na příkopě 22, metro A/B to Můstek, www.palacecinemas.cz)
Village Cinemas at Anděl (Radlická 3179/1E, metro B to Anděl, www.villagecinemas.cz)
Cinema City at the Palác Flóra (Vinohradská 144, metro A to Flóra, www.cinemacity.cz)
IMAX at the Palác Flóra (Vinohradská 144, metro A to Flóra, www.imaxpraha.cz)

Tickets cost around 170 Kč per adult, 120 Kč per child or 500 Kč per family.