Quite frankly I'm worried by few things about Werder.
1) Set pieces. From close range Micoud is pretty lethal, while Naldo and Pasanen

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have incredibly tough shots when it comes to the long range efforts. Remember how Bayern scored against Juve at Delle Alpi? Those kind of bouncy, lucky shots too form a realistic and totally unpredictable threat.
2) Their strong midfield. Dynamic Baumann won't let Vieira too much of a space, he's very underrated in my opinion. Micoud and Frings can play pretty well both ways, while Power-Pekka is an unhidden force at the bench. (Ok, the last part was a joke

) Back to the topic, Borowski is good too, they've got pretty nice depth on that department.
Things that I'm not worried about:
1) Unlike the others, I say their attack. Klasnic and specially Klose are overrated, and quite frankly I can't see Cannavaro, Émerson and Thuram having any problems with them. Valdez has quick feet, but that's it, he's not the finisher-type that clinches the big victories.
2) Their defense. Pasanen is very good stopper, but their problem is their experience. For example Naldo plays in vital position, but is still very young and prone to mistakes that they can't afford. Trezeguet simply won't have mercy. Apart from Pasanen, I've been impressed by young Owomoyela, but their other flank doesn't really impress me. Camoranesi and Zlatan can tear them apart.
Summa summarum, I'm quite confident that Juve will go through. 1-1 or 1-2 at away game and victory at Delle Alpi will see Juve going through.