I agree that the cuts were painful. I have read that the "houses of healing" scenes, in which Aragorn uses his healer's hands and Eowyn and Faramir fall in love, were filmed and than cut, so they should be in the extended version. Other stuff...who knows? I expect some discussion of Denethor's Palantir will make it into the extended cut, as it was hinted at mightily in the theatrical release.

I thought the complete absence of Aragorn's people, the Dunedain or descendants of Numenor, was sad. In the book they rally and accompany the heroes on the paths of the dead and in the corsair ships. In the movies they seem to have abandoned Aragorn entirely, as you never see another Dunedain at all. In Tolkien's universe they were an important symbol. The Woses were also eliminated, so that Gondor and Rohan are completely alone.

I also thought that Arwen's fate being tied to the ring was weird, and that they didn't have to go through the whole "now you are becoming mortal because you've finally made the decision to stay" scene. This last was unnecessary especially because they already explained in the first movie why she will not go to Valinor but Frodo will, at least to those who were paying attention: "whatever grace is given me, may it pass to him." I hate it when films decide you're not smart enough and invent dumb explanations for things (midochlorians, anyone?)

But there were also some great scenes that were not in the book, or only hinted at. Pippin lighting the first signal fire, and then the others slowly igniting, one by one across the mountains, was very inspiring. A scene between Eowyn and Theoden after the latter has been wounded and she has killed the Morgul king was also a nice addition. Some scenes in the book that would have looked silly on film, like Gollum leaping around triumphantly and simply falling into the cracks of doom, were changed as well.

In all, I thought it was a good adaptation and a great movie. The battle sequences were astounding, the human (or hobbitish) drama with Frodo and Sam and Gollum was riveting, and the acting in general outstanding. Good Job, Jackson!