Spring and fall are considered high season in Prague. Of the two, spring is the more beautiful. The magnolia trees begin to flower in early April and if you're blessed with a few sunny days, you're going to think you died and went to heaven. Fall (Sept-Oct) can be pleasant as well, with long, warm days and usually reliably sunny weather. Avoid travel over the Christmas, New Year's, and Easter holidays, when the city fills to brimming with tour groups from Germany and Italy. Midsummer (July-Aug) is considered shoulder (in-between) season. On the plus side, hotels usually discount prices 20% or more. On the minus, summers can be surprisingly iffy weather-wise. Some years bring weeks of hot sunshine; others, day after day of cold rain. You might also consider coming during the off-season: January and February and from November to mid-December. Yes, it's cold and often rainy or snowy, but the crowds thin out and you finally feel like you have this beautiful city to yourself.
The Weather -- Spring and fall generally bring the best weather for touring, with warm days and cool nights. Summers can be hit or miss, with some years bringing lots of rain and others weeklong stretches of hot sunshine. Winters can be cold and unusually long, sometimes lasting into April or even May. Rain is a possibility any time of year, so be sure to pack an umbrella.