Here's a list of the major train operator websites for major European countries, you can search times, fares and buy tickets using them:

Austria http://www.oebb.at
Belgium http://www.b-rail.be
France http://www.voyages-sncf.com
Germany http://www.bahn.de
Italy http://www.trenitalia.com
Netherlands http://www.ns.nl
Portugal http://www.cp.pt
Switzerland http://www.sbb.ch
Spain http://www.renfe.com
Sweden http://www.sj.se