If you dont have your own transport and, therefore, wont be doing pueblos, then you can easily do Cuenca in a day.
We went for a day trip by train too. The journey is really pretty (that flat rust/brown/orange bits of green landscape, that i personnally love about spain).
The historical part is quite small, but it is a fun town. We didnt go to the Ciudad Encantada, which is impressive i believe, natural rock formations that look like animals, etc. But i'm not sure how well comunicado it is with Cuenca itself. maybe someone else knows??
I agree with the suggestion that you do Avila on the way to Salamanca and that you stay longer in Salamanca than a day. there is loads to see and do and the nightlife is great. also, you may be able to go to some pueblos from there (La Alberca, Bejar, etc).
Do try and go to Valle de los Caidos, its amazing and i think its good to see other, more modern aspects of Spanish history.
Dont forget Alcala de Henares, its very pretty and only cercania ride away. We did the walking tour, ask at the tourist kiosko in the main square. It was very informative and i think we covered the most interesting sites.
Lastly, food is also an important tourist attraction! try local dishes (as well as local restaurants), as many of these towns have their own specialities!
hope these suggestions are useful to you and...
have fun! maybe i'll go touristing this weekend, you've inspired me!
"when you're not feeling holy, your loneliness says that you've sinned"<br />L. Cohen