I think the Madrid team is slightly better.
Before people accuse me of being a closet Madridista, these are my reasons:-
1) Better goalkeeper
2) Better defence
3) Better balanced midfield
Barcelona have the better front line.
Why do I think Madrid have a better defence? Well as much as Pique and Puyol are both awesome, so were Hierro and Cannavaro (cannavaro to a lesser extent). But Madrid have the better full backs definitely. Roberto Carlos was amazing and Salgado in his prime was one of, if not the best right back in the world. GVB wasn't really a top class left back and Alves is world class, but I think Madrid have a more solid backline there.
The midfield is more balanced (I didn't say better - I said better balanced) with Makelele as the DM with Zidane, Figo and Cronaldo. MAN that is a salivatin thought to see those 3 in their prime. Xaviesta is of course magnificent too. But I love that Madrid midfield. It has everything. Pace, Power, Intelligence, Craft. Everything.
Barca attack is better for sure. Dinho, Eto'o and Messi together(i.e. the 2005 dinho, the 2009 Eto'o, the 2010 Messi....awesome).
Ronaldo joined madrid at a point in his career when he was past his prime too that also made me choose the Barca front line.