And the extended version of ROTK isn't out yet, right? So you can't really make a judgment on that one.
Hmmmm... I've been thinking about your comments, Laura, and I think you do have a case for the theatrical release of The Two Towers being better than the Extended Edition. The comical antics of Merry and Pippin do seem very out of place. However, I was really impressed by the flashback scene with Faramir and Boromir so it is a bit of a hard call.
The movie is better off without any more comic relief. There was too much of it already as it was. But the flashback scene made Faramir's story more credible and added a great moment of poignancy to the film. I also enjoyed seeing more scenes with Eomer and Eowyn. I think Eomer definitely got a better introduction in the Extended Edition. Also, the scene with Aragorn and the horse was really sweet.
Gollum got more screen time too which was excellent - shame they didn't work his backstory in here though. It would have been a far more appropriate place to put it than at the opening of The Return of the King.
And they had some cool scenes with Saruman. I liked Saruman discovering that Gandalf had found the heir of Illendiul (not sure on the name exactly - anyway, Aragorn).
All in all, I think the extra material in the Extended Edition is generally very good and adds some good stuff to the film. But I could have lived without the extra Merry and Pippin comic relief scenes.
As for the Extended Edition of The Return of the King, I guarantee it will be better than the theatrical release. We'll see the death of Saruman, Gandalf's confrontation with the Witch King, a tonne of other things that we saw in the preview but were conspicuously absent in the movie - and the House of Healing.
If it isn't better, I will be very surprised. And I will eat my hat (not literally, of course).