Atlantic Portugal is probably the cheapest. Try Nazare between Lisbon and Porto, English guy called Captain Mike runs the marina, but it is a pretty desolate place. We are currently out of the water in Sopromars yard in Lagos, which is competitvely priced with the other Algarve yards. Lagos has plenty of atmosphere in the winter, go to www.marlagos.pt for current rates. Atlantic Spain is cheaper than the Algarve with a whole host of marinas. We are leaving our boat at Rota for 6weeks in the spring and it works out about 10 euros a night, look at www.puertosdeandalucia.com for rates. If you want to sail during the winter you really need to be in the Algarve or Atlantic Spain, as further north the weather is less predictable and can close certain Portugese ports for weeks.
If you plan to live on the boat, and not just park it and fly home, then you can do it here on the Rio Guadiana. It is free to anchor. There are pontoon berths in the river at about the same rate as local marinas, ie 7- 10 euros a day. But because the river floods now and then, most recently in 1997, it is not fit to leave boats unattended.