Trains, Buses and Public Transport
Czech Republic Bus and Train Schedules - handy online form to search for bus/train schedules and connections, including international; in English
Prague Public Transportation Authority - all you ever wanted to know about Prague public transportation
Prague Public Transit Schedules - schedules and connections of the metro, trams, buses; in English

Motorcycle Rental
Motorbike Ventures - they rent motorikes and can include all the necessary gear for traveling in the Czech Republic and Europe. Can also help with purchasing a motorbike in the Czech Republic.

Car Rental
Affordable Car Rental Prague
Alimex ČR
ASAP Rent Car
AVIS Czech Republic
Europcar Czech Republic
First Car Rent Company
Hertz Czech Republic
Royal Rent a Car
Toscar Rent a Car

Budget Airlines
easyJet - large UK based airline with an extensive European network, including flights to Prague from London (Gatwick and Stansted), Newcastle, East Midlands, Bristol, and Dortmund
Helvetic - Swiss budget airline based in Zurich that flies to Prague, London, Vienna and many European cities in southern Europe
Norwegian Air Shuttle - Norwegian low-fare airline that flies from Bergen, Oslo, and Trondheim to Prague
Ryanair - largest European discount carrier flies from London (Stansted) to Brno
SkyEurope - Largest Central European low-cost airline with bases in Budapest, Krakow, Warsaw, Prague and Bratislava.  Destinations from Prague (starting April 2006): Amsterdam, Barcelona, Milan, Naples, Nice, Paris, and Rome.
Smart Wings - Czech low-cost airline that flies to Prague from Amsterdam, Dublin, London, Madrid, and Rome. From May 2005 there are flights from Heraklion, Larnaca, Palma de Mallorca, and Thessaloniki.