I also use the Bahn.de website that Laurel mentioned for checking rail schedules throughout Europe. However, they only sell tickets for trains originating in Germany (with some exceptions). For more specific information and prices, the websites of the rail networks that actually operate the trains are the best source of information (ie: Trenitalia or Italo in Italy, SNCF in France, SBB in Switzerland, ÖBB in Austria, Renfe in Spain, etc.).
Depending on which countries you're travelling in, you could also use a website such as www.trainline.com as they display schedules and sell tickets for a number of rail networks in Europe, including those in France, Italy, Germany, Spain and others. In order to buy tickets on Trainline, you'll first have to register on the site and provide payment details. After that, the process is very easy. In some cases they charge a small service fee, but I don't find that to be a problem.