By Air: Prague is not yet part of the European Union, so there are not as many connections to the city as most Western European capitals enjoy. But you still have a wide range of choices. The best deals on flying to Prague are through the UK with direct flights from London, Manchester and other UK cities. See EasyJet, Czech Airlines and others for special deals that can cost as little as 100 Euros round trip including taxes.
From other destinations, there are often deals on Czech Airlines, but they change all the time, so you must check their site often for the deals that match your itinerary. Expect to pay around 150 Euros for a discounted flight from Paris, Brussels or Amsterdam, which is about half the normal price. Czech Airlines also has deals from the US to Prague, often with a stopover.
Rail: There are trains from most points on the continent to Prague, usually thru Germany. Deals usually involve either 2 or more persons traveling together (a 40% discount), or buying a railpass which offers deals for traveling in more than one country. Some of the discounts are cumulative, meaning if you’re over 65 or a student, you get an additional discount. If you travel a long distance in Europe by train it’s advisable to get a supplemental couchette (additional fee) with a bed for an overnight rest. While there are some deals on rail travel, unless you really want to travel by train, and don’t mind long journeys (over 10 hours), you’d do better to fly to Prague just to save the time. In fact my discounted airline ticket was a few euros cheaper than the train including all the applicable discounts I might’ve gotten by rail.
Car: Taking a auto into any Eastern European country is not a good idea. In fact most Western European rental companies (including the multinational ones) won’t let you drive to the Czech Republic. It’s due to several reasons, not the least of which is the number of stolen cars there. If you must travel by car, you should probably rent one when you get there. Certainly a car is no advantage within central Prague since parking and narrow streets are a problem, so unless you have other destinations that require a car to reach, I’d avoid driving in Prague.
Bus: There are several bus lines that travel to Prague including Eurolines. They offer great deals, and are often the cheapest way to get to Eastern Europe. However you’ll have to contend with a very long journey, and buses are not like trains for overall comfort on such long journeys. In addition, buses crossing borders are subject to much more delay and hassles as immigration and customs officials tend to go over buses more carefully.
Once the Czech Republic becomes part of the EU in 2004, travel should be much easier, with more connections and fewer border hassles coming and going. Not that there’s any special problem now. It’s certainly not like it was in the Communist days when travel was much more restricted and the border guards much more careful.