The situation here in Spain is not good. Bikes (other than folders packed in bags) are prohibited on most long distance routes, including the ones covered by the high speed AVE trains. They are allowed on many middle distance and local (cercanías) trains, but even on those the decision is often left up to porters, who can be quite arbitrary. I'm a member of a cycling advocacy group that has been negotiating with RENFE, the main railway company, in an effort to get them to admit more bikes, but our suggestions have fallen on deaf ears. We're now considering public protests. Anyone considering travelling here is advised to contact RENFE before making plans. I've been using buses more and more as they tend to have more progressive policies. Most bus companies require that you dismantle and pack your bike, but I've found that taking off the front wheel and wrapping any parts that might damage other people's luggage (chain, cassette...) with plastic and tape is usually sufficient.

The situation in Portugal is much different. Almost all trains (except, I believe, some of the busier ones in the Lisbon area) accept bikes. The Portuguese railway company, in fact, actually encourages bike/train travel as a greener way to go.