Portugal is the stronger team in the sense of being a team. They grind out their victories on ball possession. They lead the tournament in short passes, and they have defenders that can mark strong strikers, like Van Nistelrooy, quite well.
What they don't have is the capability to score a lot of goals, let alone to finish with good chances. To Holland's credit, they're a better team on paper. They also lead the tournament in deep passes, which might cause a lot of trouble for Portugal. And I don't give Portugal much of a home edge in this tournament -- afterall, 2/3 of the fans at the England-Portugal QF were wearing the cross of St. George and making far more noise than the "locals".
I think they're fairly matched up without a clear favorite. It's going to come down to Portugal not making stupid mistakes (see opening goals in matches against Greece, England) versus Holland's ability to stretch the field and not get frustrated.
I smell extra time here, and as much as I would prefer Portugal to win -- I'm going to pick Holland to win with a creative Van Nistelrooy goal in ET: 2-1.