Join Date: Dec 2003
Location: Brooklyn, NY, United States
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Posts: 1,735
You're not saying how long your trip is. Is it your first trip to all these cities? If so, I would spend as little time in Madrid as reasonably possible, but do give it at least 2 days.
BCN - spend as long as you can, but at list 4-5 days. But then, I'm biased, I'm in love with this city. I could stay there for a month and never get bored.
San Sebastian - a fascinating city, but in spring, you'll be missing the beach scene. Spend at least 3 days.
Fly everywhere; intra-Spain air travel can be dirt cheap.
The real question, once again, is how much time you have. If you do have some extra time, I'd consider Bilbao to the west and Biarritz in France to the east. 1.5-2 hours by bus in each direction. All three (Bilbao, San Sebastian, and Biarritz are incredibly interesting and picturesque, each in their own right, with plenty of things to see and do).
Hope it helps.