Going to Prague by bus is a mode of transport which is less and less used, namely to the development of low cost airlines that currently offer very good connections from Prague (see our post on flights to Prague).
There are probably several coach companies going to Prague, but the most reliable (and comfortable) is certainly Eurolines.
You can have a look at their website on http://www.eurolines.com/
Still, don’t forget that if you book in advance, or are simply going to buy a return ticket, you’d rather check low cost airlines first, as they will probably offer similar prices!
In fact, using a company such as Eurolines may be convenient if you’re planning on going on a backpacking trip. Then you’re going to use regularly bus connections, without having time constraints. Thus you should book a limited period of time ticket that you can use several times without having to pay more (fixed feed), and can simply hop on and hop off the bus in any destination you feel like visiting.