If want to know specific travel times or prices to and from specific cities, try this link: How to Get from City to City in Spain
Renting a Car in Spain
Is Car Rental in Spain Worth the Money?
Renting a car in Spain costs a lot more than going by public transport, so decide carefully. Renting a car in Spain can be worth it if you plan on exploring areas that aren't well covered by public transport, but for 'city hopping' use the train or bus. Read more on car rental in Spain by clicking on the above link.
Internal Flights in Spain
Which airlines fly within Spain?
If you can book your flights far enough in advance, flying within Spain can be the cheapest option. On this page you'll find the web addresses of the carriers that fly within Spain.
Bus and Train Travel in Spain
Which is better - train or bus?
If you can't get a cheap enough flight, you'll have to travel by bus or train. The train is the more luxurious of the two options, but it comes with some issues that need to be considered. See the above link to see the pros and cons of traveling by bus and train as well as a comparison of travel times and prices.
A good resource is this Interactive Map of Train Routes in Spain from Rail Europe, a company that does cheap rail passes for the whole continent. They have maps for most of Europe: European Train Routes.
Which Rail Pass?
Choosing Your Eurail & Inter Rail Pass
There is a large number of rail passes on offer so choose wisely. But make sure it will be worth the money - these things are expensive and commit you to traveling more than you might normally.
If you are under 26, your passes can be found here: Eurail & Inter Rail Passes for the Under 26s
Bus and Train Stations in Spain
"¿Donde está la estación?"
This means "Where is the station?" in Spanish. Unfortunately it isn't as simple as that, as there is often not just one station. In particular in Madrid & Barcelona have a number of bus stations: