Porto Cova..south of Setubul in Portugal..There is a portected national beach/park area in this locale and the sea/beaches/cliffs and town are crtainly off the beaten track and so beautiful. Non-touristy is tyhe only way to go.

When is this trip?
What sort of transport are you using?
How long is the trip for?
Where are you landing and going home from?
Are there any specifics you are interested in?

If you are attempting to visit Spain and Portugal in 2 weeks I'd rethink this plan. 2 weeks is not nearly enough to cover this area. If you're looking for a mix of the highlights and some less visited spots then you may want to do a more concentrated trip to a limited geography (based on your interests).

There is a bit of a flaw in your request (apart from covering too much ground in two weeks). I can recommend lovely towns in Portugal but I have no idea if they are in guide books. I suspect every one of them is so you'll have to investigate the guide books and decide if you want to visit or not.

Marvao (probably in lots of guide books)
Sao Pedro do Corval (you won't find any tourist here - there's nothing going on!!)

Most of us would like to find ideal non-touristy spots. That is almost impossible. Remember that Spain and Portugal have been subject to modern mass-tourism since the 60s. Croatia was part of Yugoslavia which a few Germans visited and then was recently in a war. Tourism isn't so well developed there, but you can bet your boots that the scribblers are busy turning out guide books, and your unlisted towns will soon be there. It's the nature of the beast. Those of us who know such towns keep them secret so they remain somewhat untouched for when we next visit.

Vast and wonderful areas of diverse Spain and Portugal are not touristy at all. Even the extremely popular south of Spain is full of places way off the beaten track and into the mountains, the marshlands etc. Take a look at Michael Jacobs "Andalucía" to get a cultural intro with lots of suggestions of places way off the "normal" route.
http://www.amazon.co.uk/Andalucia-Pallas-guides-Michael-Jacobs/dp/1873429789

I think there are towns that tourists do not visit in all countries. I've been to some of these towns in France. They are lovely but there is nothing to do if you don't live there. No market, no cafe, etc. You can walk around and look at the houses but after that is done what do you do there, particularly if you don't speak the language.

Pick a road and explore it.