There's a lot of banter between Gimli and Legolas that did make the movies in the extended editions. As it stands so far, the theatrical makes up 6 hours between the two movies, the extended makes up almost 7 and half hours. That nearly hour and half more adds a lot back into the movies from the stories.
As to Gimli's and Aragorn's little comments at Helm's Deep, I didn't mind it. Jackson was trying to inject a little bit of comedic relief, something that you don't see in a book, but not having it in a movie could end up losing the audience if you get too serious. Remember, Jackson was trying to make a film that would appeal to everyone, not just the die hard Tolkien fans, and without those occasional bits of humor, he might have lost a number of people.