ALIEN -- it's a toss-up. I love a lot of the subtle editing changes that have been made in this new version, as well as most of the deleted scenes that have been added. I can't help feel, however, that the ending (as Kegg has already noted) is interrupted in its pacing by the nest scene).
ALIENS -- The Special Edition is the superior film. I've seen the Theatrical Version once, and have no desire to see it again. It cuts out a number of key scenes that are part of Ripley's development (such as the reveal that her daughter has died of old age, or the "Ellen"/"Dwayne" scene), as well as a number of terrific action beats with the automated guns.
ALIEN 3 -- Another toss-up here. I enjoy many of the scenes that have been included in the special edition, but I'm not sure about all the other changes. The dog-burster, for example, works better than the cow. Also, the ending is better in the theatrical version, with the longer fall by Ripley (even though I like Bishop II's "I'm human" bit).
ALIEN RESURRECTION -- Yet another toss-up. The opening credits of the theatrical version are better, and some of the added material was wisely cut (I'm thinking of most of Raymond Cruz's scenes, as he is far too over-the-top). On the other hand, there's a nice moment reminding the audience of Newt that I really like, which was cut from the theatrical version.