I have 4 nights in Barcelona and then headed to San Sebastian. My wife doesn't want to fly on the small planes so we're thinking of taking a train. I was thinking would be good for an overnight, to break the trip up. Lately I've heard Zaragoza isn't worth it and I don't know what to do. Should I head straight to San Sebastian? I have 5 nights in the Basque country, three nights reserved in San Sebastian. Any recommendations on Zaragoza and/or where to spend the other two nights in the Pais Vasco would be much appreciated.

Head out straight to San Sebastian, plenty to do an see. Bilbao is wonderful; Santiago would be amazing, a bit far though. Your call if cutting a day in San Sebastian so that you can get to Santiago (this is what I would do...!).

I would head straight to wonderful San Sebastián. You just might love it so much you'll want to stay another night or two, or spend those 2 nights somewhere else on the Basque coast.
You have a large array of options of all price ranges in the Basque Country, and it shouldn't be nearly as hot on the coast as in Zaragoza, which I try to keep far away from in the summer.

Options for your extra nights:

In the Urdaibai Biosphere Reserve, between Bilbao and San Sebastián
(several lovely rural homes belonging to www.nekatur.net)

Bilbao itself and a day trip to Las Arenas/Portugalete to see the Hanging Bridge

Lekeitio, on the coast in Bizkaia

Getaria on the coast in Gipuzkoa (amazing seafood at Elkano or Kai)

Hondarribia on the coast (Gipuzkoa) near the French border

or on the French side (Pays Basque inland will be far less crowded in summer than coastal)

I do second ("even third") Maribel. Also, on Saturday morning the farmers market in Tolosa (inland) is worth. I like to buy there my beloved smoked cheese from Idiazabal, "alubias" (dark beans) and "tejas" (tiles, traditional almond cookies).
http://www.turismoa.euskadi.net/s11-...609-ficha.html

http://www.turismoa.euskadi.net/s11-...966-ficha.html

http://www.turismoa.euskadi.net/s11-...608-ficha.html

Thank you so much for the advice. Now I have five nights in the Basque country. I may spend the extra nights in Bilbao or Getaria or Hondarribia. A night in a rural spot is sounding really good. I definitely want lunch at Kai for the whole grilled Turbot. Will I need to rent a car to get there from San Sebastian?
Maribel I want to thank you for an incredible trip to Madrid, Sevilla and Granada last year thanks to your recommendations.

Egbert,
Thanks very much for your "thanks"!

If you just want to go to Getaria for lunch at Elkano or Kai, you can get there with Euskotren, which runs bus and train service along the coast.

www.euskotren.es/euskotren2/portada/ing

But if you want to stay in one of the rural guest houses of the Nekatur association, you'll need a car.

We've done a lot of rural tourism in the Basque Country and really enjoy staying in these casas rurales (like a B&B). But....They're not for everyone, since they are located in the country rather than in town, just so you'll know.

We stay in one outside of Getaria (Zumaia) but always with a car.
Ditto to the ones in the Urdaibai, some lovely properties, but you do need a car.
Also for those in the countryside around Hondarribia.

If you'd rather stay in town, in Hondarribia you have the Parador and the Hotel Obispo (which I really like) in the Old Quarter, which are an easy walk to La Marina, the fishermen's quarter and "downtown".
Hondarribia is very compact.
If you travel light of luggage, you can even get to Hondarribia from San Sebastián on the bus.

www.interbus.com.es/

To reach Bilbao from San Sebastián, you can just take the handy Pesa bus and stay downtown. Plenty of hotels there in all price ranges.
www.pesa.net

Don't know what time of year you're traveling, but if it's July/Aug. you do need reservations ASAP for Hondarribia, even for one night.
It's a very popular vacation spot for Spanish families in high season.
Not much foreign tourism at all, except for the French who come over for dining from Hendaye on the shuttle boat.
That's why we like it in high season. But off season it can be very quiet. Depends on when you plan to visit.