I think it will be either Manchester United or Real Madrid. I got to this result by elimination.
AC Milan proved in the first leg of the knock-out stage that their all-defensive style can stop the brilliance of Arsenal. They now have a very good chance to eliminate Arsenal and continue on, so Arsenal is out. However, Milan is too old, too tired and too much based on one single player (Kaka) in order to go all the way.
Inter Milan is also a strong candidate, but they are in a very weak position after their 2-0 defeat against Liverpool in Anfield. I believe that Liverpool will manage to eliminate Inter, but I don't think they're talented enough to make it to the 3rf appearance in the Finals in 4 years. In addition, Liverpool relies on Steven Gerrard in a similar way to Milan's reliance on Kaka, but Gerrard is not as good as Kaka, and the rest of the Liverpool roster is not as good as Milan's.
Barcelona and Chelsea are also forces to reckon. Both teams are in excellent position to qualify for the quarter-finals (Barcelona after an away win over Celtic and Chelsea after an away draw against Olimpiakos), but Barcelona is way to unstable this year to go beyond the semi-finals and Chelsea is not the frightening side they were in the last 2-3 seasons. They somehow lost the might that made opponents lose the faith in their ability to beat them, I think.
And so we come to the last to major candidates: Real Madrid and Manchester United. Real lost to Roma in the firtst leg of the knock-out stage, but it was a minimal defeat (2-1), and they managed to score an away goal. I think that in the Santiago Bernabeu, where Real won all of its matches this season, Roma will lose in more than 1 goal margin, and Real will qualify. Real is a very well balanced team, with numerous great players who have a very good season (Raul, Van Nistelrooy, Guti, Casillas, Sergio Ramos, Robinho). The team is not too reliant on one single player, and the so-called "backing" players (Robben, Baptista, etc.) are good enough to fill in if one of the superstars have a bad day.
Manchester United, Like Real, is a very well balanced team. Cristiano Ronaldo is a very central piece in the puzzle, but they also have Wayne Rooney, Ryan Giggs, Carlos Tevez etc. They're defense is also very solid and reliable. United, as a team, is better (I think) than the sum of all its players, and they play excellent and stable football, even though on paper, Real has a better squad. Moreover, United managed to draw theiraway game against Olympique Lyonnais (1-1), and are in an excellent position to qualify to the quarter finals. To be fair, I'm a Manchester United supporter, and I deeply hope they'll take the cup, but I think I estimated their chances more-or-less objectively.
I would like to apologize to all the supporters of Seville, Fenerbahce, Schalke and Porto for not taking their teams into account. The last three are just not good enough to make in past the quarter-finals (actually, if Schalke and Porto didn't play each other in the first knock out stage, I'd say they're not good enough teams to pass the first knock out stage. Seville is a relatively decent team, but they're still not quite in the level of the big clubs: Their squad is not strong enough, and the club is inexperienced in those levels (it's Seville's first season in the Champions' League).
And after all that, let's not forget it's football. anything can happen. Last season, I answered a very much mistaken answer to a similar question, so everyone's invited to make fun of me in 3-months time, if they wish to :)