I just ran across this excellent site. It is actually the website of Germany’s national railway, but allows you to input virtually any start and finish point in Europe and get a route, based on your entered requirements. As far as I know, this is the only site of its kind.
The next-best thing is that you can choose trains that allow bicycles on board. Considering that the rules related to bicycles are far from clear in just about any country in Europe (see this article for France), this little check box is a jewel.